From 8c886026aec97fa30001e11f79e4b105c60e4436 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Thu, 13 Jun 2024 13:00:32 +0200 Subject: [PATCH] fix the all tools jjson --- results/all_tools.json | 121431 ++++++++++++++++++++++---------------- 1 file changed, 69791 insertions(+), 51640 deletions(-) diff --git a/results/all_tools.json b/results/all_tools.json index baf7fe69..4f4fe4e2 100644 --- a/results/all_tools.json +++ b/results/all_tools.json @@ -1,51642 +1,69793 @@ [ - [ - { - "Galaxy wrapper id": "askor", - "Galaxy tool ids": [ - "askor_de" - ], - "Description": "AskoR links EdgeR and AskOmics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/askomics/askoR", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "askor_de", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", - "Galaxy wrapper version": "0.2", - "Conda id": "bioconductor-limma", - "Conda version": "3.58.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "baric_archive", - "Galaxy tool ids": [ - "baric_archive_rennes", - "baric_archive_toulouse" - ], - "Description": "A data source tool to fetch data from a BARIC Archive server.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.cesgo.org/catibaric/", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive", - "Galaxy wrapper version": "1.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "braker", - "Galaxy tool ids": [ - "braker" - ], - "Description": "BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Gaius-Augustus/BRAKER", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "braker", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", - "Galaxy wrapper version": "2.1.6", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "braker3", - "Galaxy tool ids": [ - "braker3" - ], - "Description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .", - "bio.tool id": "braker3", - "bio.tool ids": [ - "braker3" - ], - "biii": null, - "bio.tool name": "BRAKER3", - "bio.tool description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes", - "EDAM operation": [ - "Genome annotation", - "Gene prediction" - ], - "EDAM topic": [ - "RNA-Seq", - "Genomics", - "Structure prediction", - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/Gaius-Augustus/BRAKER", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "braker3", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker3", - "Galaxy wrapper version": "3.0.8", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Genome annotation", - "Gene prediction" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Genomics", - "Structure prediction", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "feelnc2asko", - "Galaxy tool ids": [ - "feelnc2asko" - ], - "Description": "Convert FeelNC GTF to GFF3", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/tderrien/FEELnc", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "feelnc2asko", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko", - "Galaxy wrapper version": "0.1", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gcms2isocor", - "Galaxy tool ids": [ - "gcms2isocor" - ], - "Description": "Conversion from GCMS PostRun Analysis to Isocor", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "gcms2isocor", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor", - "Galaxy wrapper version": "0.1.0", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "get_pairs", - "Galaxy tool ids": [ - "get_pairs" - ], - "Description": "Separate paired and unpaired reads from two fastq files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "get_pairs", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs", - "Galaxy wrapper version": "0.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "helixer", - "Galaxy tool ids": [ - "helixer" - ], - "Description": "Gene calling with Deep Neural Networks", - "bio.tool id": "helixer", - "bio.tool ids": [ - "helixer" - ], - "biii": null, - "bio.tool name": "Helixer", - "bio.tool description": "Deep Learning to predict gene annotations", - "EDAM operation": [ - "Gene prediction", - "Genome annotation" - ], - "EDAM topic": [ - "Sequence analysis", - "Gene transcripts" - ], - "Status": "To update", - "Source": "https://github.com/weberlab-hhu/Helixer", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "helixer", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/helixer", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/helixer", - "Galaxy wrapper version": "0.3.3", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Gene prediction", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Gene transcripts" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "logol", - "Galaxy tool ids": [ - "logol_wrapper" - ], - "Description": "Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://logol.genouest.org/web/app.php/logol", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/logol", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/logol", - "Galaxy wrapper version": "1.7.8", - "Conda id": "logol", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "meneco", - "Galaxy tool ids": [ - "meneco" - ], - "Description": "Meneco computes minimal completions to your draft network with reactions from a repair network", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://bioasp.github.io/meneco/", - "ToolShed categories": [ - "Systems Biology" - ], - "ToolShed id": "meneco", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/meneco", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/meneco", - "Galaxy wrapper version": "1.5.2", - "Conda id": "meneco", - "Conda version": "1.5.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "miranda2asko", - "Galaxy tool ids": [ - "miranda2asko" - ], - "Description": "Converts miRanda output into AskOmics format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "miranda2asko", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko", - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko", - "Galaxy wrapper version": "0.2", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "openlabcds2csv", - "Galaxy tool ids": [ - "openlabcds2csv" - ], - "Description": "Creates a summary of several \"Internal Standard Report\" OpenLabCDS results.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "openlabcds2csv", - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv", - "Galaxy wrapper version": "0.1.0", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "peptimapper", - "Galaxy tool ids": [ - "peptimapper_clustqualify", - "peptimapper_clust_to_gff", - "peptimapper_pep_match", - "peptimapper_pep_novo_tag" - ], - "Description": "Proteogenomics workflow for the expert annotation of eukaryotic genomes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "genouest", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper", - "Galaxy wrapper version": "2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "Ensembl-REST", - "Galaxy tool ids": [ - "get_feature_info", - "get_genetree", - "get_sequences" - ], - "Description": "A suite of Galaxy tools designed to work with Ensembl REST API.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://rest.ensembl.org", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST", - "Galaxy wrapper version": "0.1.2", - "Conda id": "requests", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "GAFA", - "Galaxy tool ids": [ - "gafa" - ], - "Description": "Gene Align and Family Aggregator", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://aequatus.tgac.ac.uk", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "gafa", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA", - "Galaxy wrapper version": "0.3.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "TreeBest", - "Galaxy tool ids": [ - "treebest_best" - ], - "Description": "TreeBeST best", - "bio.tool id": "treebest", - "bio.tool ids": [ - "treebest" - ], - "biii": null, - "bio.tool name": "TreeBeST", - "bio.tool description": "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.", - "EDAM operation": [ - "Phylogenetic tree visualisation", - "Phylogenetic analysis", - "Phylogenetic inference (from molecular sequences)" - ], - "EDAM topic": [ - "Phylogenetics" - ], - "Status": "To update", - "Source": "http://treesoft.sourceforge.net/treebest.shtml", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "treebest_best", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest", - "Galaxy wrapper version": "1.9.2.post0", - "Conda id": "treebest", - "Conda version": "1.9.2.post1", - "EDAM operation (no superclasses)": [ - "Phylogenetic tree visualisation", - "Phylogenetic inference (from molecular sequences)" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "apoc", - "Galaxy tool ids": [ - "apoc" - ], - "Description": "Large-scale structural comparison of protein pockets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://cssb.biology.gatech.edu/APoc", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "apoc", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc", - "Galaxy wrapper version": "1.0+galaxy1", - "Conda id": "apoc", - "Conda version": "1b16", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast_parser", - "Galaxy tool ids": [ - "blast_parser" - ], - "Description": "Convert 12- or 24-column BLAST output into 3-column hcluster_sg input", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/TGAC/earlham-galaxytools/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "blast_parser", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser", - "Galaxy wrapper version": "0.1.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ete", - "Galaxy tool ids": [ - "ete_gene_csv_finder", - "ete_genetree_splitter", - "ete_homology_classifier", - "ete_init_taxdb", - "ete_lineage_generator", - "ete3_mod", - "ete_species_tree_generator" - ], - "Description": "Analyse phylogenetic trees using the ETE Toolkit", - "bio.tool id": "ete", - "bio.tool ids": [ - "ete" - ], - "biii": null, - "bio.tool name": "ete", - "bio.tool description": "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", - "EDAM operation": [ - "Phylogenetic analysis", - "Phylogenetic tree editing" - ], - "EDAM topic": [ - "Phylogenetics" - ], - "Status": "To update", - "Source": "http://etetoolkit.org/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "ete", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete", - "Galaxy wrapper version": "3.1.2", - "Conda id": "ete3", - "Conda version": "3.1.1", - "EDAM operation (no superclasses)": [ - "Phylogenetic tree editing" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 7 - }, - { - "Galaxy wrapper id": "export_to_cluster", - "Galaxy tool ids": [ - "export_to_cluster" - ], - "Description": "Export datasets to cluster", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/TGAC/earlham-galaxytools/", - "ToolShed categories": [ - "Data Export" - ], - "ToolShed id": "export_to_cluster", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster", - "Galaxy wrapper version": "0.0.2", - "Conda id": "EXPORT_DIR_PREFIX", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gblocks", - "Galaxy tool ids": [ - "gblocks" - ], - "Description": "Gblocks", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://molevol.cmima.csic.es/castresana/Gblocks.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gblocks", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks", - "Galaxy wrapper version": "0.91b", - "Conda id": "gblocks", - "Conda version": "0.91b", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gstf_preparation", - "Galaxy tool ids": [ - "gstf_preparation" - ], - "Description": "GeneSeqToFamily preparation converts data for the workflow", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/TGAC/earlham-galaxytools/", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "gstf_preparation", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation", - "Galaxy wrapper version": "0.4.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hcluster_sg", - "Galaxy tool ids": [ - "hcluster_sg" - ], - "Description": "Hierarchically clustering on a sparse graph", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/douglasgscofield/hcluster", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "hcluster_sg", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg", - "Galaxy wrapper version": "0.5.1.1", - "Conda id": "hcluster_sg", - "Conda version": "0.5.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hcluster_sg_parser", - "Galaxy tool ids": [ - "hcluster_sg_parser" - ], - "Description": "Converts hcluster_sg 3-column output into lists of ids", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/TGAC/earlham-galaxytools/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "hcluster_sg_parser", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser", - "Galaxy wrapper version": "0.2.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lotus2", - "Galaxy tool ids": [ - "lotus2" - ], - "Description": "LotuS2 OTU processing pipeline", - "bio.tool id": "lotus2", - "bio.tool ids": [ - "lotus2" - ], - "biii": null, - "bio.tool name": "lotus2", - "bio.tool description": "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.", - "EDAM operation": [ - "Sequence feature detection", - "DNA barcoding" - ], - "EDAM topic": [ - "Metagenomics", - "Taxonomy", - "Microbial ecology" - ], - "Status": "Up-to-date", - "Source": "http://lotus2.earlham.ac.uk/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "lotus2", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2", - "Galaxy wrapper version": "2.32", - "Conda id": "lotus2", - "Conda version": "2.32", - "EDAM operation (no superclasses)": [ - "Sequence feature detection", - "DNA barcoding" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Taxonomy", - "Microbial ecology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "miranda", - "Galaxy tool ids": [ - "miranda" - ], - "Description": "Finds potential target sites for miRNAs in genomic sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.microrna.org/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "miranda", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda", - "Galaxy wrapper version": "3.3a+galaxy1", - "Conda id": "miranda", - "Conda version": "3.3a", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "plotheatmap", - "Galaxy tool ids": [ - "plotheatmap" - ], - "Description": "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.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "plotheatmap", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap", - "Galaxy wrapper version": "1.0", - "Conda id": "bioconductor-preprocesscore", - "Conda version": "1.64.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rdock", - "Galaxy tool ids": [ - "rdock" - ], - "Description": "Docking ligands to proteins and nucleic acids", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rdock.sourceforge.net/", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "rdock", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock", - "Galaxy wrapper version": "1.0", - "Conda id": "rDock", - "Conda version": "2013.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "replace_chromosome_names", - "Galaxy tool ids": [ - "replace_chromosome_names" - ], - "Description": "Replace chromosome names", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "replace_chromosome_names", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names", - "Galaxy wrapper version": "0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rsat_filter_snps", - "Galaxy tool ids": [ - "rsat_filter_snps" - ], - "Description": "Filter SNPs in RSAT Matrix Scan output", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/TGAC/earlham-galaxytools/", - "ToolShed categories": [ - "ChIP-seq", - "Systems Biology" - ], - "ToolShed id": "rsat_filter_snps", - "Galaxy wrapper owner": "earlham", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smart_domains", - "Galaxy tool ids": [ - "smart_domains" - ], - "Description": "SMART domains", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://smart.embl.de/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "smart_domains", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains", - "Galaxy wrapper version": "0.1.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smina", - "Galaxy tool ids": [ - "smina" - ], - "Description": "smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://sourceforge.net/projects/smina/", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "smina", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina", - "Galaxy wrapper version": "1.0", - "Conda id": "smina", - "Conda version": "2017.11.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "t_coffee", - "Galaxy tool ids": [ - "t_coffee" - ], - "Description": "T-Coffee", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.tcoffee.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "t_coffee", - "Galaxy wrapper owner": "earlhaminst", - "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee", - "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee", - "Galaxy wrapper version": "13.45.0.4846264", - "Conda id": "t-coffee", - "Conda version": "13.46.0.919e8c6b", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "abacas", - "Galaxy tool ids": [ - "abacas" - ], - "Description": "Order and Orientate Contigs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/abacas", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "abacas", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/abacas", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas", - "Galaxy wrapper version": "1.1", - "Conda id": "mummer", - "Conda version": "3.23", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "assemblystats", - "Galaxy tool ids": [ - "assemblystats" - ], - "Description": "Summarise an assembly (e.g. N50 metrics)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "assemblystats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats", - "Galaxy wrapper version": "1.1.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bam2mappingstats", - "Galaxy tool ids": [ - "bam2mappingstats" - ], - "Description": "Generates mapping stats from a bam file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "bam2mappingstats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats", - "Galaxy wrapper version": "1.1.0", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bamclipper", - "Galaxy tool ids": [ - "bamclipper" - ], - "Description": "Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/tommyau/bamclipper", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bamclipper", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/tommyau/bamclipper", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bamclipper", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biohansel", - "Galaxy tool ids": [ - "biohansel" - ], - "Description": "Heidelberg and Enteritidis SNP Elucidation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/biohansel", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "biohansel", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/biohansel", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel", - "Galaxy wrapper version": "2.4.0", - "Conda id": "bio_hansel", - "Conda version": "2.6.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biohansel_bionumeric_converter", - "Galaxy tool ids": [ - "bionumeric_convert" - ], - "Description": "Convert BioHansel output data to a Bionumerics friendly form", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "biohansel_bionumeric_converter", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter", - "Galaxy wrapper version": "0.2.0", - "Conda id": "pandas", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bundle_collections", - "Galaxy tool ids": [ - "bundle_collection" - ], - "Description": "Tool to bundle up list collection into a single zip to be download", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bundle_collections", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections", - "Galaxy wrapper version": "1.3.0", - "Conda id": "perl-getopt-long", - "Conda version": "2.54", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "collapse_collection", - "Galaxy tool ids": [ - "collapse_dataset" - ], - "Description": "Collection tool that collapses a list of files into a single datasset in order of appears in collection", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "collapse_collections", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection", - "Galaxy wrapper version": "5.1.0", - "Conda id": "gawk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "combineJSON", - "Galaxy tool ids": [ - "combine_json" - ], - "Description": "JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "combine_json", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "combine_assembly_stats", - "Galaxy tool ids": [ - "combine_stats" - ], - "Description": "Combine multiple Assemblystats datasets into a single tabular report", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "combine_assemblystats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats", - "Galaxy wrapper version": "1.0", - "Conda id": "perl-getopt-long", - "Conda version": "2.54", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "combine_tabular_collection", - "Galaxy tool ids": [ - "combine" - ], - "Description": "Combine Tabular Collection into a single file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "combine_tabular_collection", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "concat_paired", - "Galaxy tool ids": [ - "concat_fastqs" - ], - "Description": "Concatenate paired datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/concat", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "concat_paired", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/concat", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired", - "Galaxy wrapper version": "0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cryptogenotyper", - "Galaxy tool ids": [ - "CryptoGenotyper" - ], - "Description": "CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/CryptoGenotyper", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "cryptogenotyper", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/CryptoGenotyper", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper", - "Galaxy wrapper version": "1.0", - "Conda id": "cryptogenotyper", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "csvtk", - "Galaxy tool ids": [ - "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" - ], - "Description": "Rapid data investigation and manipulation of csv/tsv files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioinf.shenwei.me/csvtk/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "csvtk", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/shenwei356/csvtk", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk", - "Galaxy wrapper version": "0.20.0", - "Conda id": "csvtk", - "Conda version": "0.30.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ectyper", - "Galaxy tool ids": [ - "ectyper" - ], - "Description": "EC-Typer - in silico serotyping of Escherichia coli species", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/ecoli_serotyping", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ectyper", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/ecoli_serotyping", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper", - "Galaxy wrapper version": "1.0.0", - "Conda id": "ectyper", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta2bed", - "Galaxy tool ids": [ - "fasta2bed" - ], - "Description": "Convert multiple fasta file into tabular bed file format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fasta2bed", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed", - "Galaxy wrapper version": "1.0.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_extract", - "Galaxy tool ids": [ - "fa-extract-sequence" - ], - "Description": "extract single fasta from multiple fasta file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fasta_extract", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract", - "Galaxy wrapper version": "1.1.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastqc_stats", - "Galaxy tool ids": [ - "FastQC_Summary" - ], - "Description": "Summary multiple FastQC into a single tabular line report", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fastqc_stats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats", - "Galaxy wrapper version": "1.2", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "feht", - "Galaxy tool ids": [ - "feht" - ], - "Description": "Automatically identify makers predictive of groups.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "feht", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht", - "Galaxy wrapper version": "0.1.0", - "Conda id": "feht", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_spades_repeats", - "Galaxy tool ids": [ - "filter_spades_repeat" - ], - "Description": "Remove short and repeat contigs/scaffolds", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "filter_spades_repeats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats", - "Galaxy wrapper version": "1.0.1", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "getmlst", - "Galaxy tool ids": [ - "getmlst" - ], - "Description": "Download MLST datasets by species from pubmlst.org", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "getmlst", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst", - "Galaxy wrapper version": "0.1.4.1", - "Conda id": "srst2", - "Conda version": "0.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gnali", - "Galaxy tool ids": [ - "gnali" - ], - "Description": "A tool to find nonessential, loss-of-function gene variants", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/gnali/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "gnali", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/gnali/", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali", - "Galaxy wrapper version": "1.1.0", - "Conda id": "gnali", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hivtrace", - "Galaxy tool ids": [ - "hivtrace" - ], - "Description": "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.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "hivtrace", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace", - "Galaxy wrapper version": "1.0.1", - "Conda id": "hivtrace", - "Conda version": "1.5.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kaptive", - "Galaxy tool ids": [ - "kaptive" - ], - "Description": "Kaptive reports information about capsular (K) loci found in genome assemblies.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "kaptive", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive", - "Galaxy wrapper version": "0.3.0", - "Conda id": "kaptive", - "Conda version": "3.0.0b1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kat_filter", - "Galaxy tool ids": [ - "kat_@EXECUTABLE@" - ], - "Description": "Filtering kmers or reads from a database of kmers hashes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "kat_filter", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter", - "Galaxy wrapper version": "2.3", - "Conda id": "kat", - "Conda version": "2.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kat_sect", - "Galaxy tool ids": [ - "kat_@EXECUTABLE@" - ], - "Description": "SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "kat_sect", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect", - "Galaxy wrapper version": "2.3", - "Conda id": "kat", - "Conda version": "2.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mauve_contig_mover", - "Galaxy tool ids": [ - "mauve_contig_mover" - ], - "Description": "Order a draft genome relative to a related reference genome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/mauve_contig_mover", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mauve_contig_mover", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/mauve_contig_mover", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover", - "Galaxy wrapper version": "1.0.10", - "Conda id": "mauve", - "Conda version": "2.4.0.r4736", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mob_suite", - "Galaxy tool ids": [ - "mob_recon", - "mob_typer" - ], - "Description": "MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/mob-suite", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mob_suite", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/mob-suite", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite", - "Galaxy wrapper version": "3.0.3", - "Conda id": "mob_suite", - "Conda version": "3.1.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "mrbayes", - "Galaxy tool ids": [ - "mrbayes" - ], - "Description": "A program for the Bayesian estimation of phylogeny.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mrbayes", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes", - "Galaxy wrapper version": "1.0.2", - "Conda id": "mrbayes", - "Conda version": "3.2.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mykrobe_parser", - "Galaxy tool ids": [ - "mykrobe_parseR" - ], - "Description": "RScript to parse the results of mykrobe predictor.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/mykrobe-parser", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mykrobe_parser", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/mykrobe-parser", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser", - "Galaxy wrapper version": "0.1.4.1", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pangolin", - "Galaxy tool ids": [ - "pangolin" - ], - "Description": "Phylogenetic Assignment of Named Global Outbreak LINeages", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/hCoV-2019/pangolin", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pangolin", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/hCoV-2019/pangolin", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin", - "Galaxy wrapper version": "1.1.14", - "Conda id": "pangolin", - "Conda version": "4.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "patrist", - "Galaxy tool ids": [ - "patrist" - ], - "Description": "Extract Patristic Distance From a Tree", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "patrist", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/patrist", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist", - "Galaxy wrapper version": "0.1.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plasmid_profiler", - "Galaxy tool ids": [ - "plasmid_profiler" - ], - "Description": "Explores plasmid content in WGS data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "plasmid_profiler", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler", - "Galaxy wrapper version": "0.1.6", - "Conda id": "r", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plasmid_profiler_suite", - "Galaxy tool ids": [], - "Description": "Plasmid Profiler suite defining all dependencies for Plasmid Profiler", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "suite_plasmid_profiler", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plasmidspades", - "Galaxy tool ids": [ - "plasmidspades" - ], - "Description": "Genome assembler for assemblying plasmid", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "plasmidspades", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades", - "Galaxy wrapper version": "1.1", - "Conda id": "spades", - "Conda version": "4.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pneumocat", - "Galaxy tool ids": [ - "pneumocat" - ], - "Description": "Pneumococcal Capsular Typing of illumina fastq reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phe-bioinformatics/PneumoCaT", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pneumocat", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phe-bioinformatics/PneumoCaT", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat", - "Galaxy wrapper version": "1.2.1", - "Conda id": "pneumocat", - "Conda version": "1.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "promer", - "Galaxy tool ids": [ - "promer4_substitutions" - ], - "Description": "Aligns two sets of contigs and reports amino acid substitutions between them", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/promer", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "promer", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/promer", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer", - "Galaxy wrapper version": "1.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pseudogenome", - "Galaxy tool ids": [ - "pseudogenome" - ], - "Description": "Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pseudogenome", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome", - "Galaxy wrapper version": "1.0.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "quasitools", - "Galaxy tool ids": [ - "aacoverage", - "aavariants", - "callcodonvar", - "callntvar", - "complexity_bam", - "complexity_fasta", - "consensus", - "distance", - "dnds", - "drmutations", - "hydra", - "quality" - ], - "Description": "A collection of tools for analysing Viral Quasispecies", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/quasitools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "quasitools", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/quasitools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools", - "Galaxy wrapper version": "0.7.0", - "Conda id": "quasitools", - "Conda version": "0.7.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "refseq_masher", - "Galaxy tool ids": [ - "refseq_masher_contains", - "refseq_masher_matches" - ], - "Description": "Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/refseq_masher", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "refseq_masher", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/refseq_masher", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher", - "Galaxy wrapper version": "0.1.2", - "Conda id": "refseq_masher", - "Conda version": "0.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "seqtk_nml", - "Galaxy tool ids": [ - "seqtk_nml_sample" - ], - "Description": "Tool to downsample fastq reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/lh3/seqtk", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seqtk_nml", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml", - "Galaxy wrapper version": "1.0.1", - "Conda id": "seqtk", - "Conda version": "1.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sistr_cmd", - "Galaxy tool ids": [ - "sistr_cmd" - ], - "Description": "SISTR in silico serotyping tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/sistr_cmd", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sistr_cmd", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd", - "Galaxy wrapper version": "1.1.1", - "Conda id": "sistr_cmd", - "Conda version": "1.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smalt", - "Galaxy tool ids": [ - "smalt" - ], - "Description": "SMALT aligns DNA sequencing reads with a reference genome.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://www.sanger.ac.uk/science/tools/smalt-0", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "smalt", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://sourceforge.net/projects/smalt/", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt", - "Galaxy wrapper version": "0.7.6", - "Conda id": "smalt", - "Conda version": "0.7.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spades_header_fixer", - "Galaxy tool ids": [ - "spades_header_fixer" - ], - "Description": "Fixes Spades Fasta ids", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/galaxy_tools", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "spades_fasta_header_fixer", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer", - "Galaxy wrapper version": "1.1.2+galaxy1", - "Conda id": "sed", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spatyper", - "Galaxy tool ids": [ - "spatyper" - ], - "Description": "Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/HCGB-IGTP/spaTyper", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "spatyper", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper", - "Galaxy wrapper version": "0.3.3", - "Conda id": "spatyper", - "Conda version": "0.3.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spolpred", - "Galaxy tool ids": [ - "spolpred" - ], - "Description": "A program for predicting the spoligotype from raw sequence reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "spolpred", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred", - "Galaxy wrapper version": "1.0.1", - "Conda id": "spolpred", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "srst2", - "Galaxy tool ids": [ - "srst2" - ], - "Description": "Short Read Sequence Typing for Bacterial Pathogens", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "srst2", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2", - "Galaxy wrapper version": "0.3.7", - "Conda id": "srst2", - "Conda version": "0.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "staramr", - "Galaxy tool ids": [ - "staramr_search" - ], - "Description": "Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/staramr", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "staramr", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr", - "Galaxy wrapper version": "0.10.0", - "Conda id": "staramr", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "stringmlst", - "Galaxy tool ids": [ - "stringmlst" - ], - "Description": "Rapid and accurate identification of the sequence type (ST)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "stringmlst", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst", - "Galaxy wrapper version": "1.1.0", - "Conda id": "stringMLST", - "Conda version": "0.6.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tree_relabeler", - "Galaxy tool ids": [ - "tree_relabel" - ], - "Description": "Relabels the tips of a newick formatted tree.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "tree_relabeler", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler", - "Galaxy wrapper version": "1.1.0", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "wade", - "Galaxy tool ids": [ - "wade" - ], - "Description": "identify regions of interest", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/phac-nml/wade", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "wade", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/wade", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade", - "Galaxy wrapper version": "0.2.5+galaxy1", - "Conda id": "wade", - "Conda version": "0.2.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "camera", - "Galaxy tool ids": [ - "abims_CAMERA_annotateDiffreport", - "abims_CAMERA_combinexsAnnos" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "camera", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera", - "Galaxy wrapper version": "1.48.0", - "Conda id": "r-snow", - "Conda version": "0.4_1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "correlation_analysis", - "Galaxy tool ids": [ - "correlation_analysis" - ], - "Description": "[Metabolomics][W4M] Metabolites Correlation Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "correlation_analysis", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis", - "Galaxy wrapper version": "1.0.1+galaxy0", - "Conda id": "r-batch", - "Conda version": "1.1_4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gcms2isocor", - "Galaxy tool ids": [ - "gcms2isocor" - ], - "Description": "Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/p2m2/p2m2tools", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "gcms2isocor", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor", - "Galaxy wrapper version": "0.2.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "genform", - "Galaxy tool ids": [ - "genform" - ], - "Description": "genform: generation of molecular formulas by high-resolution MS and MS/MS data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://sourceforge.net/projects/genform/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "genform", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform", - "Galaxy wrapper version": null, - "Conda id": "genform", - "Conda version": "r8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "influx_data_manager", - "Galaxy tool ids": [ - "influx_data_manager" - ], - "Description": "Handling influx_si data inputs in Galaxy workflows", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "influx_si_data_manager", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager", - "Galaxy wrapper version": "1.0.2", - "Conda id": "influx-si-data-manager", - "Conda version": "1.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "influx_si", - "Galaxy tool ids": [ - "influx_si" - ], - "Description": "metabolic flux estimation based on [in]stationary labeling", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/sgsokol/influx", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "influx_si", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si", - "Galaxy wrapper version": "7.0.1", - "Conda id": "influx_si", - "Conda version": "7.0.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ipo", - "Galaxy tool ids": [ - "ipo4retgroup", - "ipo4xcmsSet" - ], - "Description": "[W4M][LC-MS] IPO", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/rietho/IPO", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "ipo", - "Galaxy wrapper owner": "lecorguille", - "Galaxy wrapper source": "https://github.com/rietho/IPO", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo", - "Galaxy wrapper version": "1.10.0", - "Conda id": "bioconductor-ipo", - "Conda version": "1.28.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "isoplot", - "Galaxy tool ids": [ - "isoplot" - ], - "Description": "Isoplot is a software for the visualisation of MS data from C13 labelling experiments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metabolomics", - "Visualization" - ], - "ToolShed id": "isoplot", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/llegregam/Isoplot/tree/main", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot", - "Galaxy wrapper version": "1.3.0+galaxy1", - "Conda id": "isoplot", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "kmd_hmdb_data_plot", - "Galaxy tool ids": [ - "kmd_hmdb_data_plot" - ], - "Description": "retrieves data from KMD HMDB API and produce plot and csv file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/workflow4metabolomics/tools-metabolomics", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "kmd_hmdb_data_plot", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot", - "Galaxy wrapper version": "1.0.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mixmodel4repeated_measures", - "Galaxy tool ids": [ - "mixmodel4repeated_measures" - ], - "Description": "[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "mixmodel4repeated_measures", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures", - "Galaxy wrapper version": "3.1.0", - "Conda id": "r-lme4", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ms2snoop", - "Galaxy tool ids": [ - "ms2snoop" - ], - "Description": "[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "ms2snoop", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop", - "Galaxy wrapper version": "2.2.1", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nmr_annotation", - "Galaxy tool ids": [ - "NmrAnnotation" - ], - "Description": "[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "nmr_annotation", - "Galaxy wrapper owner": "marie-tremblay-metatoul", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/nmr_annotation", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation", - "Galaxy wrapper version": "3.0.0", - "Conda id": "r-batch", - "Conda version": "1.1_4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nmr_annotation2d", - "Galaxy tool ids": [ - "2DNmrAnnotation" - ], - "Description": "[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "2dnmrannotation", - "Galaxy wrapper owner": "marie-tremblay-metatoul", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d", - "Galaxy wrapper version": "2.0.0", - "Conda id": "r-batch", - "Conda version": "1.1_4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nmr_preprocessing", - "Galaxy tool ids": [ - "NMR_Preprocessing", - "NMR_Read" - ], - "Description": "[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "nmr_preprocessing", - "Galaxy wrapper owner": "marie-tremblay-metatoul", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/nmr_preprocessing", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing", - "Galaxy wrapper version": null, - "Conda id": "r-batch", - "Conda version": "1.1_4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "normalization", - "Galaxy tool ids": [ - "normalization" - ], - "Description": "[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://workflow4metabolomics.org", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "normalization", - "Galaxy wrapper owner": "marie-tremblay-metatoul", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/normalization", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization", - "Galaxy wrapper version": "1.0.7", - "Conda id": "r-batch", - "Conda version": "1.1_4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "physiofit", - "Galaxy tool ids": [ - "physiofit" - ], - "Description": "PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "physiofit.readthedocs.io", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "physiofit", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/MetaSys-LISBP/PhysioFit", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit", - "Galaxy wrapper version": "3.3.5", - "Conda id": "physiofit", - "Conda version": "3.3.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "physiofit_manager", - "Galaxy tool ids": [ - "physiofit_data_manager" - ], - "Description": "Handling of physiofit input files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "physiofit_manager", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager", - "Galaxy wrapper version": "1.0.1", - "Conda id": "physiofit_data_manager", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "skyline2isocor", - "Galaxy tool ids": [ - "skyline2isocor" - ], - "Description": "Converting skyline output to IsoCor input", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "skyline2isocor", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor", - "Galaxy wrapper version": "1.0.0", - "Conda id": "skyline2isocor", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "xcms", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/sneumann/xcms", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "xcms", - "Galaxy wrapper owner": "workflow4metabolomics", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/", - "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms", - "Galaxy wrapper version": "3.12.0", - "Conda id": "bioconductor-xcms", - "Conda version": "4.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 9, - "Available on UseGalaxy.org.au": 9, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 10 - }, - { - "Galaxy wrapper id": "apollo", - "Galaxy tool ids": [ - "create_account", - "feat_from_gff3", - "create_or_update", - "delete_features", - "delete_organism", - "export", - "fetch_jbrowse", - "iframe", - "list_organism" - ], - "Description": "Access an Apollo instance from Galaxy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxy-genome-annotation/python-apollo", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo", - "Galaxy wrapper version": null, - "Conda id": "apollo", - "Conda version": "4.2.13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 9, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "askomics", - "Galaxy tool ids": [ - "askomics_integrate" - ], - "Description": "Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/askomics/", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics", - "Galaxy wrapper version": null, - "Conda id": "askocli", - "Conda version": "0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chado", - "Galaxy tool ids": [ - "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" - ], - "Description": "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", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxy-genome-annotation/python-chado", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado", - "Galaxy wrapper version": null, - "Conda id": "python-chado", - "Conda version": "2.3.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "genenotebook", - "Galaxy tool ids": [ - "genenotebook_build" - ], - "Description": "Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://genenotebook.github.io", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook", - "Galaxy wrapper version": "0.4.15", - "Conda id": "genoboo", - "Conda version": "0.4.15", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "jbrowse", - "Galaxy tool ids": [ - "jbrowse_to_container" - ], - "Description": "A tool allowing to export a JBrowse dataset into a JBrowse docker container", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://jbrowse.org", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": "jbrowse_to_container", - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse", - "Galaxy wrapper version": null, - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "repeatexplorer2", - "Galaxy tool ids": [ - "repeatexplorer_clustering" - ], - "Description": "Tool for annotation of repeats from unassembled shotgun reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/repeatexplorer/repex_tarean", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "repeatexplorer2", - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2", - "Galaxy wrapper version": "2.3.8", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tripal", - "Galaxy tool ids": [ - "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" - ], - "Description": "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", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxy-genome-annotation/python-tripal", - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "gga", - "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal", - "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal", - "Galaxy wrapper version": null, - "Conda id": "python-tripal", - "Conda version": "3.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "w4mcorcov", - "Galaxy tool ids": [ - "w4mcorcov" - ], - "Description": "OPLS-DA Contrasts of Univariate Results", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "w4mcorcov", - "Galaxy wrapper owner": "eschen42", - "Galaxy wrapper source": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master", - "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov", - "Galaxy wrapper version": "0.98.18", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "w4mclassfilter", - "Galaxy tool ids": [ - "w4mclassfilter" - ], - "Description": "Filter W4M data by values or metadata", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "w4mclassfilter", - "Galaxy wrapper owner": "eschen42", - "Galaxy wrapper source": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master", - "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter", - "Galaxy wrapper version": "0.98.19", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "w4mjoinpn", - "Galaxy tool ids": [ - "w4mjoinpn" - ], - "Description": "Join positive- and negative-mode W4M datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "w4mjoinpn", - "Galaxy wrapper owner": "eschen42", - "Galaxy wrapper source": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master", - "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn", - "Galaxy wrapper version": "0.98.2", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "batched_lastz", - "Galaxy tool ids": [ - "batched_lastz" - ], - "Description": "Galaxy wrapper for the batching Lastz runs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/gsneha26/SegAlign", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "batched_lastz", - "Galaxy wrapper owner": "richard-burhans", - "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz", - "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz", - "Galaxy wrapper version": "1.04.22", - "Conda id": "lastz", - "Conda version": "1.04.22", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ncbi_fcs_adaptor", - "Galaxy tool ids": [ - "ncbi_fcs_adaptor" - ], - "Description": "FCS-adaptor detects adaptor and vector contamination in genome sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ncbi/fcs", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ncbi_fcs_adaptor", - "Galaxy wrapper owner": "richard-burhans", - "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor", - "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor", - "Galaxy wrapper version": "0.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "segalign", - "Galaxy tool ids": [ - "segalign" - ], - "Description": "A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/gsneha26/SegAlign", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "segalign", - "Galaxy wrapper owner": "richard-burhans", - "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign", - "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign", - "Galaxy wrapper version": "0.1.2.2", - "Conda id": "segalign-full", - "Conda version": "0.1.2.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "suite_qiime2__alignment", - "Galaxy tool ids": [ - "qiime2__alignment__mafft", - "qiime2__alignment__mafft_add", - "qiime2__alignment__mask" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-alignment", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "suite_qiime2__composition", - "Galaxy tool ids": [ - "qiime2__composition__add_pseudocount", - "qiime2__composition__ancom", - "qiime2__composition__ancombc", - "qiime2__composition__da_barplot", - "qiime2__composition__tabulate" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-composition", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "suite_qiime2__cutadapt", - "Galaxy tool ids": [ - "qiime2__cutadapt__demux_paired", - "qiime2__cutadapt__demux_single", - "qiime2__cutadapt__trim_paired", - "qiime2__cutadapt__trim_single" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-cutadapt", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "suite_qiime2__dada2", - "Galaxy tool ids": [ - "qiime2__dada2__denoise_ccs", - "qiime2__dada2__denoise_paired", - "qiime2__dada2__denoise_pyro", - "qiime2__dada2__denoise_single" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://benjjneb.github.io/dada2/", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "suite_qiime2__deblur", - "Galaxy tool ids": [ - "qiime2__deblur__denoise_16S", - "qiime2__deblur__denoise_other", - "qiime2__deblur__visualize_stats" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/biocore/deblur", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "suite_qiime2__demux", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-demux", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "suite_qiime2__diversity", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-diversity", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 21, - "Available on UseGalaxy.org.au": 21, - "Available on UseGalaxy.eu": 21, - "Available on UseGalaxy.org.fr": 21 - }, - { - "Galaxy wrapper id": "suite_qiime2__diversity_lib", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-diversity-lib", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 12, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 12, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "suite_qiime2__emperor", - "Galaxy tool ids": [ - "qiime2__emperor__biplot", - "qiime2__emperor__plot", - "qiime2__emperor__procrustes_plot" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://emperor.microbio.me", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "suite_qiime2__feature_classifier", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-feature-classifier", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 10, - "Available on UseGalaxy.org.au": 10, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 10 - }, - { - "Galaxy wrapper id": "suite_qiime2__feature_table", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-feature-table", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 17, - "Available on UseGalaxy.org.au": 17, - "Available on UseGalaxy.eu": 17, - "Available on UseGalaxy.org.fr": 17 - }, - { - "Galaxy wrapper id": "suite_qiime2__fragment_insertion", - "Galaxy tool ids": [ - "qiime2__fragment_insertion__classify_otus_experimental", - "qiime2__fragment_insertion__filter_features", - "qiime2__fragment_insertion__sepp" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-fragment-insertion", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "suite_qiime2__longitudinal", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-longitudinal", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 11, - "Available on UseGalaxy.org.au": 11, - "Available on UseGalaxy.eu": 11, - "Available on UseGalaxy.org.fr": 11 - }, - { - "Galaxy wrapper id": "suite_qiime2__metadata", - "Galaxy tool ids": [ - "qiime2__metadata__distance_matrix", - "qiime2__metadata__merge", - "qiime2__metadata__shuffle_groups", - "qiime2__metadata__tabulate" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-metadata", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "suite_qiime2__phylogeny", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-phylogeny", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 12, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 12, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "suite_qiime2__quality_control", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-quality-control", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "suite_qiime2__quality_filter", - "Galaxy tool ids": [ - "qiime2__quality_filter__q_score" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-quality-filter", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "suite_qiime2__rescript", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nbokulich/RESCRIPt", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "suite_qiime2__sample_classifier", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-sample-classifier", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 15, - "Available on UseGalaxy.org.au": 15, - "Available on UseGalaxy.eu": 15, - "Available on UseGalaxy.org.fr": 15 - }, - { - "Galaxy wrapper id": "suite_qiime2__taxa", - "Galaxy tool ids": [ - "qiime2__taxa__barplot", - "qiime2__taxa__collapse", - "qiime2__taxa__filter_seqs", - "qiime2__taxa__filter_table" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-taxa", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "suite_qiime2__vsearch", - "Galaxy tool ids": [ - "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" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/qiime2/q2-vsearch", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch", - "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 8, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 7 - }, - { - "Galaxy wrapper id": "suite_qiime2_core__tools", - "Galaxy tool ids": [ - "qiime2_core__tools__export", - "qiime2_core__tools__import", - "qiime2_core__tools__import_fastq" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://qiime2.org", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools", - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools", - "Galaxy wrapper version": "2024.5.0+dist.he540b0b0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "suite_qiime2_core", - "Galaxy tool ids": [], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics", - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "q2d2", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - } - ], - [ - { - "Galaxy wrapper id": "add_value", - "Galaxy tool ids": [ - "addValue" - ], - "Description": "Add a value as a new column.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "add_value", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value", - "Galaxy wrapper version": "1.0.1", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "annotation_profiler", - "Galaxy tool ids": [ - "Annotation_Profiler_0" - ], - "Description": "Profile Annotations for a set of genomic intervals", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "annotation_profiler", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "best_regression_subsets", - "Galaxy tool ids": [ - "BestSubsetsRegression1" - ], - "Description": "Perform Best-subsets Regression", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "best_regression_subsets", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets", - "Galaxy wrapper version": "1.0.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "blat_coverage_report", - "Galaxy tool ids": [ - "generate_coverage_report" - ], - "Description": "Polymorphism of the Reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers", - "Sequence Analysis" - ], - "ToolShed id": "blat_coverage_report", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blat_mapping", - "Galaxy tool ids": [ - "blat2wig" - ], - "Description": "Coverage of the Reads in wiggle format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers", - "Sequence Analysis" - ], - "ToolShed id": "blat_mapping", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bowtie_wrappers", - "Galaxy tool ids": [ - "bowtie_wrapper" - ], - "Description": "Galaxy wrappers for the Bowtie short read mapping tools.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bowtie-bio.sourceforge.net/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "bowtie_wrappers", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers", - "Galaxy wrapper version": "1.2.0", - "Conda id": "bowtie", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "canonical_correlation_analysis", - "Galaxy tool ids": [ - "cca1" - ], - "Description": "Canonical Correlation Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "canonical_correlation_analysis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis", - "Galaxy wrapper version": "1.0.0", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "categorize_elements_satisfying_criteria", - "Galaxy tool ids": [ - "categorize_elements_satisfying_criteria" - ], - "Description": "Categorize Elements satisfying criteria.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "categorize_elements_satisfying_criteria", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ccat", - "Galaxy tool ids": [ - "peakcalling_ccat" - ], - "Description": "Control-based ChIP-seq Analysis Tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "ccat", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat", - "Galaxy wrapper version": "0.0.2", - "Conda id": "ccat", - "Conda version": "3.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cd_hit_dup", - "Galaxy tool ids": [ - "cd_hit_dup" - ], - "Description": "simple tool for removing duplicates from sequencing reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": "cd_hit_dup", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup", - "Galaxy wrapper version": "0.0.1", - "Conda id": "cd-hit-auxtools", - "Conda version": "4.8.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "change_case", - "Galaxy tool ids": [ - "ChangeCase" - ], - "Description": "Convert column case.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "change_case", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case", - "Galaxy wrapper version": "1.0.1", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "compute_motif_frequencies_for_all_motifs", - "Galaxy tool ids": [ - "compute_motif_frequencies_for_all_motifs" - ], - "Description": "Compute Motif Frequencies For All Motifs, motif by motif.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": "compute_motif_frequencies_for_all_motifs", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "compute_motifs_frequency", - "Galaxy tool ids": [ - "compute_motifs_frequency" - ], - "Description": "Compute Motif Frequencies in indel flanking regions.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": "compute_motifs_frequency", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "compute_q_values", - "Galaxy tool ids": [ - "compute_q_values" - ], - "Description": "Compute q-values based on multiple simultaneous tests p-values", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "compute_q_values", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "condense_characters", - "Galaxy tool ids": [ - "Condense characters1" - ], - "Description": "Condense consecutive characters.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "condense_characters", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "convert_characters", - "Galaxy tool ids": [ - "Convert characters1" - ], - "Description": "Convert delimiters to tab.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "convert_characters", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "convert_solid_color2nuc", - "Galaxy tool ids": [ - "color2nuc" - ], - "Description": "Convert Color Space to Nucleotides", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "convert_solid_color2nuc", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "correlation", - "Galaxy tool ids": [ - "cor2" - ], - "Description": "Correlation for numeric columns", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "correlation", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "count_gff_features", - "Galaxy tool ids": [ - "count_gff_features" - ], - "Description": "Count GFF Features", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "count_gff_features", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features", - "Galaxy wrapper version": "0.2", - "Conda id": "galaxy-ops", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ctd_batch", - "Galaxy tool ids": [ - "ctdBatch_1" - ], - "Description": "CTD analysis of chemicals, diseases, or genes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ctd_batch", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cummerbund", - "Galaxy tool ids": [ - "cummeRbund" - ], - "Description": "Wrapper for the Bioconductor cummeRbund library", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/cummeRbund.html", - "ToolShed categories": [ - "RNA", - "Visualization" - ], - "ToolShed id": "cummerbund", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund", - "Galaxy wrapper version": "2.16.0", - "Conda id": "fonts-conda-ecosystem", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cummerbund_to_tabular", - "Galaxy tool ids": [ - "cummerbund_to_cuffdiff" - ], - "Description": "Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats", - "Next Gen Mappers" - ], - "ToolShed id": "cummerbund_to_tabular", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular", - "Galaxy wrapper version": "1.0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cut_columns", - "Galaxy tool ids": [ - "Cut1" - ], - "Description": "Select columns from a dataset.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "cut_columns", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns", - "Galaxy wrapper version": "1.0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "delete_overlapping_indels", - "Galaxy tool ids": [ - "delete_overlapping_indels" - ], - "Description": "Delete Overlapping Indels from a chromosome indels file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "delete_overlapping_indels", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dgidb_annotator", - "Galaxy tool ids": [ - "dgidb_annotate" - ], - "Description": "Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Systems Biology", - "Variant Analysis" - ], - "ToolShed id": "dgidb_annotator", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "divide_pg_snp", - "Galaxy tool ids": [ - "dividePgSnp" - ], - "Description": "Separate pgSnp alleles into columns", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "divide_pg_snp", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "draw_stacked_barplots", - "Galaxy tool ids": [ - "draw_stacked_barplots" - ], - "Description": "Draw Stacked Bar Plots for different categories and different criteria", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "draw_stacked_barplots", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots", - "Galaxy wrapper version": "1.0.0", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "dwt_cor_ava_perclass", - "Galaxy tool ids": [ - "compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" - ], - "Description": "Compute P-values and Correlation Coefficients for Feature Occurrences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "dwt_cor_ava_perclass", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass", - "Galaxy wrapper version": "1.0.1", - "Conda id": "r-waveslim", - "Conda version": "1.7.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dwt_cor_avb_all", - "Galaxy tool ids": [ - "compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" - ], - "Description": "Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "dwt_cor_avb_all", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all", - "Galaxy wrapper version": "1.0.1", - "Conda id": "r-waveslim", - "Conda version": "1.7.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dwt_ivc_all", - "Galaxy tool ids": [ - "compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" - ], - "Description": "Compute P-values and Second Moments for Feature Occurrences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "dwt_ivc_all", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all", - "Galaxy wrapper version": "1.0.1", - "Conda id": "r-waveslim", - "Conda version": "1.7.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dwt_var_perclass", - "Galaxy tool ids": [ - "compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" - ], - "Description": "Compute P-values and Max Variances for Feature Occurrences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "dwt_var_perclass", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass", - "Galaxy wrapper version": "1.0.1", - "Conda id": "r-waveslim", - "Conda version": "1.7.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dwt_var_perfeature", - "Galaxy tool ids": [ - "dwt_var1" - ], - "Description": "Wavelet variance using Discrete Wavelet Transfoms", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "dwt_var_perfeature", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature", - "Galaxy wrapper version": "1.0.2", - "Conda id": "r-bitops", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "express", - "Galaxy tool ids": [ - "express" - ], - "Description": "Quantify the abundances of a set of target sequences from sampled subsequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "express", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/express", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/express", - "Galaxy wrapper version": "1.1.1", - "Conda id": "eXpress", - "Conda version": "1.5.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_compute_length", - "Galaxy tool ids": [ - "fasta_compute_length" - ], - "Description": "Compute sequence length", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_compute_length", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length", - "Galaxy wrapper version": "1.0.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fasta_concatenate_by_species", - "Galaxy tool ids": [ - "fasta_concatenate0" - ], - "Description": "Concatenate FASTA alignment by species", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_concatenate_by_species", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species", - "Galaxy wrapper version": "0.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fasta_filter_by_length", - "Galaxy tool ids": [ - "fasta_filter_by_length" - ], - "Description": "Filter sequences by length", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_filter_by_length", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length", - "Galaxy wrapper version": "1.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fasta_to_tabular", - "Galaxy tool ids": [ - "fasta2tab" - ], - "Description": "FASTA-to-Tabular converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_to_tabular", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular", - "Galaxy wrapper version": "1.1.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_trimmer_by_quality", - "Galaxy tool ids": [ - "fastq_quality_trimmer" - ], - "Description": "FASTQ Quality Trimmer by sliding window", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_trimmer_by_quality", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastqsolexa_to_fasta_qual", - "Galaxy tool ids": [ - "fastqsolexa_to_fasta_qual" - ], - "Description": "FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats", - "Fastq Manipulation" - ], - "ToolShed id": "fastqsolexa_to_fasta_qual", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "featurecounter", - "Galaxy tool ids": [ - "featureCoverage1" - ], - "Description": "Feature coverage", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "featurecounter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter", - "Galaxy wrapper version": "2.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_transcripts_via_tracking", - "Galaxy tool ids": [ - "filter_combined_via_tracking" - ], - "Description": "Filter Combined Transcripts", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "filter_transcripts_via_tracking", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "generate_pc_lda_matrix", - "Galaxy tool ids": [ - "generate_matrix_for_pca_and_lda1" - ], - "Description": "Generate a Matrix for using PC and LDA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "generate_pc_lda_matrix", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "getindelrates_3way", - "Galaxy tool ids": [ - "indelRates_3way" - ], - "Description": "Estimate Indel Rates for 3-way alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "getindelrates_3way", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "getindels_2way", - "Galaxy tool ids": [ - "getIndels_2way" - ], - "Description": "Fetch Indels from pairwise alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "getindels_2way", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way", - "Galaxy wrapper version": "1.0.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gmaj", - "Galaxy tool ids": [ - "gmaj_1" - ], - "Description": "GMAJ Multiple Alignment Viewer", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "gmaj", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj", - "Galaxy wrapper version": "2.0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "hisat", - "Galaxy tool ids": [ - "hisat" - ], - "Description": "HISAT is a fast and sensitive spliced alignment program.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://ccb.jhu.edu/software/hisat/index.shtml", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hisat", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat", - "Galaxy wrapper version": "1.0.3", - "Conda id": "hisat", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "histogram", - "Galaxy tool ids": [ - "histogram_rpy" - ], - "Description": "Histogram of a numeric column", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "histogram", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram", - "Galaxy wrapper version": "1.0.4", - "Conda id": "rpy2", - "Conda version": "2.7.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "indels_3way", - "Galaxy tool ids": [ - "indels_3way" - ], - "Description": "Fetch Indels from 3-way alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "indels_3way", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way", - "Galaxy wrapper version": "1.0.3", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kernel_canonical_correlation_analysis", - "Galaxy tool ids": [ - "kcca1" - ], - "Description": "Kernel Canonical Correlation Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "kernel_canonical_correlation_analysis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "kernel_principal_component_analysis", - "Galaxy tool ids": [ - "kpca1" - ], - "Description": "Kernel Principal Component Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "kernel_principal_component_analysis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "lastz_paired_reads", - "Galaxy tool ids": [ - "lastz_paired_reads_wrapper" - ], - "Description": "Galaxy wrapper for the Lastz alignment tool on paired reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "lastz_paired_reads", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads", - "Galaxy wrapper version": "1.1.1", - "Conda id": "lastz", - "Conda version": "1.04.22", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lda_analysis", - "Galaxy tool ids": [ - "lda_analy1" - ], - "Description": "Perform Linear Discriminant Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "lda_analysis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "linear_regression", - "Galaxy tool ids": [ - "LinearRegression1" - ], - "Description": "Perform Linear Regression", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "linear_regression", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "logistic_regression_vif", - "Galaxy tool ids": [ - "LogisticRegression" - ], - "Description": "Perform Logistic Regression with vif", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis", - "Statistics" - ], - "ToolShed id": "logistic_regression_vif", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif", - "Galaxy wrapper version": "1.0.1", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "maf_cpg_filter", - "Galaxy tool ids": [ - "cpgFilter" - ], - "Description": "Mask CpG/non-CpG sites from MAF file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "maf_cpg_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mapping_to_ucsc", - "Galaxy tool ids": [ - "mapToUCSC" - ], - "Description": "Format mapping data as UCSC custom track", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Visualization", - "Convert Formats", - "Next Gen Mappers" - ], - "ToolShed id": "mapping_to_ucsc", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "megablast_xml_parser", - "Galaxy tool ids": [ - "megablast_xml_parser" - ], - "Description": "Parse blast XML output", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers", - "Convert Formats" - ], - "ToolShed id": "megablast_xml_parser", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "merge_cols", - "Galaxy tool ids": [ - "mergeCols1" - ], - "Description": "Merge columns together.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "merge_cols", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols", - "Galaxy wrapper version": "1.0.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "microsatellite_birthdeath", - "Galaxy tool ids": [ - "microsatellite_birthdeath" - ], - "Description": "Identify microsatellite births and deaths", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "microsatellite_birthdeath", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "microsats_alignment_level", - "Galaxy tool ids": [ - "microsats_align1" - ], - "Description": "Extract Orthologous Microsatellites from pair-wise alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "microsats_alignment_level", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level", - "Galaxy wrapper version": "1.0.0", - "Conda id": "sputnik", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "microsats_mutability", - "Galaxy tool ids": [ - "microsats_mutability1" - ], - "Description": "Estimate microsatellite mutability by specified attributes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "microsats_mutability", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability", - "Galaxy wrapper version": "1.1.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mine", - "Galaxy tool ids": [ - "maximal_information_based_nonparametric_exploration" - ], - "Description": "Maximal Information-based Nonparametric Exploration", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "mine", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine", - "Galaxy wrapper version": "0.0.1", - "Conda id": "MINE", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "multispecies_orthologous_microsats", - "Galaxy tool ids": [ - "multispecies_orthologous_microsats" - ], - "Description": "Extract orthologous microsatellites", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "multispecies_orthologous_microsats", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-sputnik", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mutate_snp_codon", - "Galaxy tool ids": [ - "mutate_snp_codon_1" - ], - "Description": "Mutate Codons with SNPs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "mutate_snp_codon", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "partialr_square", - "Galaxy tool ids": [ - "partialRsq" - ], - "Description": "Compute partial R square", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "partialr_square", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square", - "Galaxy wrapper version": "1.0.0", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pearson_correlation", - "Galaxy tool ids": [ - "Pearson_and_apos_Correlation1" - ], - "Description": "Pearson and apos Correlation between any two numeric columns", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "pearson_correlation", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pgsnp2gd_snp", - "Galaxy tool ids": [ - "pgSnp2gd_snp" - ], - "Description": "Convert from pgSnp to gd_snp", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pgsnp2gd_snp", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pileup_interval", - "Galaxy tool ids": [ - "pileup_interval" - ], - "Description": "Pileup-to-Interval condenses pileup format into ranges of bases", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "pileup_interval", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval", - "Galaxy wrapper version": "1.0.3", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pileup_parser", - "Galaxy tool ids": [ - "pileup_parser" - ], - "Description": "Filter pileup on coverage and SNPs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-devteam/", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "pileup_parser", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser", - "Galaxy wrapper version": "1.0.2", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "plot_from_lda", - "Galaxy tool ids": [ - "plot_for_lda_output1" - ], - "Description": "Draw ROC plot on \"Perform LDA\" output", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "plot_from_lda", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "principal_component_analysis", - "Galaxy tool ids": [ - "pca1" - ], - "Description": "Principal Component Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "principal_component_analysis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis", - "Galaxy wrapper version": "1.0.2", - "Conda id": "rpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "quality_filter", - "Galaxy tool ids": [ - "qualityFilter" - ], - "Description": "Filter nucleotides based on quality scores", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "quality_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter", - "Galaxy wrapper version": "1.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rcve", - "Galaxy tool ids": [ - "rcve1" - ], - "Description": "Compute RCVE", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "rcve", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve", - "Galaxy wrapper version": "1.0.0", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "remove_beginning", - "Galaxy tool ids": [ - "Remove beginning1" - ], - "Description": "Remove lines from the beginning of a file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "remove_beginning", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rmap", - "Galaxy tool ids": [ - "rmap_wrapper" - ], - "Description": "RMAP for Solexa Short Reads Alignment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "rmap", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rmap", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rmapq", - "Galaxy tool ids": [ - "rmapq_wrapper" - ], - "Description": "RMAPQ for Solexa Short Reads Alignment with Quality Scores", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "rmapq", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rmap", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sam2interval", - "Galaxy tool ids": [ - "sam2interval" - ], - "Description": "Convert SAM to interval.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "sam2interval", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval", - "Galaxy wrapper version": "1.0.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "sam_bitwise_flag_filter", - "Galaxy tool ids": [ - "sam_bw_filter" - ], - "Description": "Filter SAM on bitwise flag values", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "sam_bitwise_flag_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "scatterplot", - "Galaxy tool ids": [ - "scatterplot_rpy" - ], - "Description": "Scatterplot of two numeric columns", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "scatterplot", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot", - "Galaxy wrapper version": "1.0.3", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "short_reads_figure_high_quality_length", - "Galaxy tool ids": [ - "hist_high_quality_score" - ], - "Description": "Histogram of high quality score reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Graphics" - ], - "ToolShed id": "short_reads_figure_high_quality_length", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length", - "Galaxy wrapper version": "1.0.0", - "Conda id": "rpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "short_reads_figure_score", - "Galaxy tool ids": [ - "quality_score_distribution" - ], - "Description": "Build base quality distribution", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Graphics" - ], - "ToolShed id": "short_reads_figure_score", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score", - "Galaxy wrapper version": "1.0.2", - "Conda id": "fontconfig", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "short_reads_trim_seq", - "Galaxy tool ids": [ - "trim_reads" - ], - "Description": "Select high quality segments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "short_reads_trim_seq", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "show_beginning", - "Galaxy tool ids": [ - "Show beginning1" - ], - "Description": "Select lines from the beginning of a file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "show_beginning", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "show_tail", - "Galaxy tool ids": [ - "Show tail1" - ], - "Description": "Select lines from the end of a file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "show_tail", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "sicer", - "Galaxy tool ids": [ - "peakcalling_sicer" - ], - "Description": "Statistical approach for the Identification of ChIP-Enriched Regions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://home.gwu.edu/~wpeng/Software.htm", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "sicer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer", - "Galaxy wrapper version": "1.1", - "Conda id": "SICER", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "split_paired_reads", - "Galaxy tool ids": [ - "split_paired_reads" - ], - "Description": "Split paired end reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "split_paired_reads", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "substitution_rates", - "Galaxy tool ids": [ - "subRate1" - ], - "Description": "Estimate substitution rates for non-coding regions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "substitution_rates", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "substitutions", - "Galaxy tool ids": [ - "substitutions1" - ], - "Description": "Fetch substitutions from pairwise alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "substitutions", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions", - "Galaxy wrapper version": "1.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "t_test_two_samples", - "Galaxy tool ids": [ - "t_test_two_samples" - ], - "Description": "T Test for Two Samples", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "t_test_two_samples", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "table_annovar", - "Galaxy tool ids": [ - "table_annovar" - ], - "Description": "Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "table_annovar", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar", - "Galaxy wrapper version": "0.2", - "Conda id": "annovar", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tabular_to_fasta", - "Galaxy tool ids": [ - "tab2fasta" - ], - "Description": "Tabular-to-FASTA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "tabular_to_fasta", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta", - "Galaxy wrapper version": "1.1.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tophat", - "Galaxy tool ids": [ - "tophat" - ], - "Description": "Tophat for Illumina", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA", - "Next Gen Mappers" - ], - "ToolShed id": "tophat", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat", - "Galaxy wrapper version": "1.5.0", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tophat2", - "Galaxy tool ids": [ - "tophat2" - ], - "Description": "Tophat - fast splice junction mapper for RNA-Seq reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://ccb.jhu.edu/software/tophat/index.shtml", - "ToolShed categories": [ - "RNA", - "Next Gen Mappers" - ], - "ToolShed id": "tophat2", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2", - "Galaxy wrapper version": "2.1.1", - "Conda id": "bowtie2", - "Conda version": "2.5.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tophat_fusion_post", - "Galaxy tool ids": [ - "tophat_fusion_post" - ], - "Description": "Wrapper for Tophat-Fusion post step", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "tophat_fusion_post", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post", - "Galaxy wrapper version": "0.1", - "Conda id": "blast+", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "trimmer", - "Galaxy tool ids": [ - "trimmer" - ], - "Description": "Trim leading or trailing characters.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "trimmer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer", - "Galaxy wrapper version": "0.0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ucsc_custom_track", - "Galaxy tool ids": [ - "build_ucsc_custom_track_1" - ], - "Description": "Build custom track for UCSC genome browser", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ucsc_custom_track", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "varscan_version_2", - "Galaxy tool ids": [ - "varscan" - ], - "Description": "VarScan wrapper", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://dkoboldt.github.io/varscan/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "varscan_version_2", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2", - "Galaxy wrapper version": "2.4.2", - "Conda id": "varscan", - "Conda version": "2.4.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcf2pgsnp", - "Galaxy tool ids": [ - "vcf2pgSnp" - ], - "Description": "VCF to pgSnp", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcf2pgsnp", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf_annotate", - "Galaxy tool ids": [ - "vcf_annotate" - ], - "Description": "Annotate a VCF file (dbSNP, hapmap)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcf_annotate", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf_extract", - "Galaxy tool ids": [ - "vcf_extract" - ], - "Description": "Extract reads from a specified region", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcf_extract", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf_filter", - "Galaxy tool ids": [ - "vcf_filter" - ], - "Description": "Filter a VCF file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcf_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf_intersect", - "Galaxy tool ids": [ - "vcf_intersect" - ], - "Description": "Generate the intersection of two VCF files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcf_intersect", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "weightedaverage", - "Galaxy tool ids": [ - "wtavg" - ], - "Description": "Assign weighted-average of the values of features overlapping an interval", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "weightedaverage", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage", - "Galaxy wrapper version": "1.0.1", - "Conda id": "galaxy-ops", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "windowsplitter", - "Galaxy tool ids": [ - "winSplitter" - ], - "Description": "Make windows", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "windowsplitter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter", - "Galaxy wrapper version": "1.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "xy_plot", - "Galaxy tool ids": [ - "XY_Plot_1" - ], - "Description": "Plotting tool for multiple series and graph types", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Statistics" - ], - "ToolShed id": "xy_plot", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot", - "Galaxy wrapper version": "1.0.2", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "basecoverage", - "Galaxy tool ids": [ - "gops_basecoverage_1" - ], - "Description": "Base Coverage of all intervals", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "basecoverage", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cluster", - "Galaxy tool ids": [ - "gops_cluster_1" - ], - "Description": "Cluster the intervals of a dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "cluster", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "complement", - "Galaxy tool ids": [ - "gops_complement_1" - ], - "Description": "Complement intervals of a dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "complement", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "concat", - "Galaxy tool ids": [ - "gops_concat_1" - ], - "Description": "Concatenate two bed files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "concat", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat", - "Galaxy wrapper version": "1.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "coverage", - "Galaxy tool ids": [ - "gops_coverage_1" - ], - "Description": "Coverage of a set of intervals on second set of intervals", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "coverage", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "flanking_features", - "Galaxy tool ids": [ - "flanking_features_1" - ], - "Description": "Fetch closest non-overlapping feature for every interval", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "flanking_features", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features", - "Galaxy wrapper version": "4.0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "get_flanks", - "Galaxy tool ids": [ - "get_flanks1" - ], - "Description": "Get flanks returns flanking region/s for every gene", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "get_flanks", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "intersect", - "Galaxy tool ids": [ - "gops_intersect_1" - ], - "Description": "Intersect the intervals of two datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "intersect", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "join", - "Galaxy tool ids": [ - "gops_join_1" - ], - "Description": "Join the intervals of two datasets side-by-side", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "join", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "merge", - "Galaxy tool ids": [ - "gops_merge_1" - ], - "Description": "Merge the overlapping intervals of a dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "merge", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "subtract", - "Galaxy tool ids": [ - "gops_subtract_1" - ], - "Description": "Subtract the intervals of two datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "subtract", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "subtract_query", - "Galaxy tool ids": [ - "subtract_query1" - ], - "Description": "Subtract Whole Dataset from another dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "subtract_query", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query", - "Galaxy wrapper version": "0.1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tables_arithmetic_operations", - "Galaxy tool ids": [ - "tables_arithmetic_operations" - ], - "Description": "Arithmetic Operations on tables", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/gops", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "tables_arithmetic_operations", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations", - "Galaxy wrapper version": "1.0.0", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "hgv_fundo", - "Galaxy tool ids": [ - "hgv_funDo" - ], - "Description": "FunDO human genes associated with disease terms", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "hgv_fundo", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hgv_hilbertvis", - "Galaxy tool ids": [ - "hgv_hilbertvis" - ], - "Description": "HVIS visualization of genomic data with the Hilbert curve", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ebi.ac.uk/huber-srv/hilbert/", - "ToolShed categories": [ - "Graphics", - "Visualization" - ], - "ToolShed id": "hgv_hilbertvis", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis", - "Galaxy wrapper version": "1.0.0", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snpfreq", - "Galaxy tool ids": [ - "hgv_snpFreq" - ], - "Description": "snpFreq significant SNPs in case-control data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis", - "Statistics" - ], - "ToolShed id": "snpfreq", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq", - "Galaxy wrapper version": "1.0.1", - "Conda id": "R", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "find_diag_hits", - "Galaxy tool ids": [ - "find_diag_hits" - ], - "Description": "Find diagnostic hits", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "find_diag_hits", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits", - "Galaxy wrapper version": "1.0.0", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gi2taxonomy", - "Galaxy tool ids": [ - "Fetch Taxonomic Ranks" - ], - "Description": "Fetch taxonomic representation", - "bio.tool id": "gi2taxonomy", - "bio.tool ids": [ - "gi2taxonomy" - ], - "biii": null, - "bio.tool name": "gi2taxonomy", - "bio.tool description": "The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).", - "EDAM operation": [ - "Database search", - "ID mapping" - ], - "EDAM topic": [ - "Taxonomy" - ], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "gi2taxonomy", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy", - "Galaxy wrapper version": "1.1.1", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [ - "Database search", - "ID mapping" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kraken2tax", - "Galaxy tool ids": [ - "Kraken2Tax" - ], - "Description": "Convert Kraken output to Galaxy taxonomy data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kraken2tax", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax", - "Galaxy wrapper version": "1.2+galaxy0", - "Conda id": "gawk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lca_wrapper", - "Galaxy tool ids": [ - "lca1" - ], - "Description": "Find lowest diagnostic rank", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "lca_wrapper", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper", - "Galaxy wrapper version": "1.0.1", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "poisson2test", - "Galaxy tool ids": [ - "poisson2test" - ], - "Description": "Poisson two-sample test", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Statistics", - "Metagenomics" - ], - "ToolShed id": "poisson2test", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test", - "Galaxy wrapper version": "1.0.0", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "t2ps", - "Galaxy tool ids": [ - "Draw_phylogram" - ], - "Description": "Draw phylogeny", - "bio.tool id": "t2ps", - "bio.tool ids": [ - "t2ps" - ], - "biii": null, - "bio.tool name": "Draw phylogeny", - "bio.tool description": "\"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format.\" - Galaxy tool wrapper", - "EDAM operation": [ - "Phylogenetic tree visualisation" - ], - "EDAM topic": [ - "Phylogenomics" - ], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "t2ps", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps", - "Galaxy wrapper version": "1.0.0", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [ - "Phylogenetic tree visualisation" - ], - "EDAM topic (no superclasses)": [ - "Phylogenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "t2t_report", - "Galaxy tool ids": [ - "t2t_report" - ], - "Description": "Summarize taxonomy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/natefoo/taxonomy", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "t2t_report", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report", - "Galaxy wrapper version": "1.0.0", - "Conda id": "taxonomy", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcftools_annotate", - "Galaxy tool ids": [ - "vcftools_annotate" - ], - "Description": "Annotate VCF using custom/user-defined annotations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_annotate", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate", - "Galaxy wrapper version": "0.1", - "Conda id": "echo", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcftools_compare", - "Galaxy tool ids": [ - "vcftools_compare" - ], - "Description": "Compare VCF files to get overlap and uniqueness statistics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_compare", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare", - "Galaxy wrapper version": "0.1", - "Conda id": "tabix", - "Conda version": "1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcftools_consensus", - "Galaxy tool ids": [ - "vcftools_consensus" - ], - "Description": "Apply VCF variants to a fasta file to create consensus sequence", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_consensus", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus", - "Galaxy wrapper version": "0.1.11", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcftools_isec", - "Galaxy tool ids": [ - "vcftools_isec" - ], - "Description": "Intersect multiple VCF datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_isec", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec", - "Galaxy wrapper version": "0.1.1", - "Conda id": "tabix", - "Conda version": "1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcftools_merge", - "Galaxy tool ids": [ - "vcftools_merge" - ], - "Description": "Merge multiple VCF datasets into a single dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_merge", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge", - "Galaxy wrapper version": "0.1.11", - "Conda id": "tabix", - "Conda version": "1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcftools_slice", - "Galaxy tool ids": [ - "vcftools_slice" - ], - "Description": "Subset VCF dataset by genomic regions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_slice", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice", - "Galaxy wrapper version": "0.1", - "Conda id": "echo", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcftools_subset", - "Galaxy tool ids": [ - "vcftools_subset" - ], - "Description": "Select samples from a VCF dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://vcftools.github.io/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcftools_subset", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset", - "Galaxy wrapper version": "0.1", - "Conda id": "tabix", - "Conda version": "1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "10x_bamtofastq", - "Galaxy tool ids": [ - "10x_bamtofastq" - ], - "Description": "Converts 10x Genomics BAM to FASTQ", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/10XGenomics/bamtofastq", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "10x_bamtofastq", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq", - "Galaxy wrapper version": "1.4.1", - "Conda id": "10x_bamtofastq", - "Conda version": "1.4.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "AggregateAlignments", - "Galaxy tool ids": [ - "graphclust_aggregate_alignments" - ], - "Description": "Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_aggregate_alignments", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments", - "Galaxy wrapper version": "0.6.0", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "AlignCluster", - "Galaxy tool ids": [ - "graphclust_align_cluster" - ], - "Description": "Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_align_cluster", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster", - "Galaxy wrapper version": "0.1", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "CMFinder", - "Galaxy tool ids": [ - "cmFinder" - ], - "Description": "Determines consensus motives for sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_cmfinder", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder", - "Galaxy wrapper version": "0.4", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "CollectResults", - "Galaxy tool ids": [ - "glob_report" - ], - "Description": "Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_postprocessing", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults", - "Galaxy wrapper version": "0.5", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "CollectResultsNoAlign", - "Galaxy tool ids": [ - "graphclust_glob_report_no_align" - ], - "Description": "Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_postprocessing_no_align", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign", - "Galaxy wrapper version": "0.5", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "GSPAN", - "Galaxy tool ids": [ - "gspan" - ], - "Description": "Second step of GraphClust", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_fasta_to_gspan", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN", - "Galaxy wrapper version": "0.4", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "LocARNAGraphClust", - "Galaxy tool ids": [ - "locarna_best_subtree" - ], - "Description": "MLocARNA computes a multiple sequence-structure alignment of RNA sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_mlocarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust", - "Galaxy wrapper version": "0.4", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "NSPDK", - "Galaxy tool ids": [ - "NSPDK_candidateClust", - "nspdk_sparse" - ], - "Description": "Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_nspdk", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK", - "Galaxy wrapper version": "9.2.3.1", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "Plotting", - "Galaxy tool ids": [ - "motifFinderPlot" - ], - "Description": "Plotting results for GraphClust", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_motif_finder_plot", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting", - "Galaxy wrapper version": "0.4", - "Conda id": "seaborn", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "PrepareForMlocarna", - "Galaxy tool ids": [ - "preMloc" - ], - "Description": "This tool prepares files for locarna step.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_prepocessing_for_mlocarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna", - "Galaxy wrapper version": "0.4", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "Preprocessing", - "Galaxy tool ids": [ - "preproc" - ], - "Description": "Preprocessing input for GraphClust", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust_preprocessing", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing", - "Galaxy wrapper version": "0.5", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "Structure_GSPAN", - "Galaxy tool ids": [ - "structure_to_gspan" - ], - "Description": "Convert RNA structure to GSPAN graphs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "structure_to_gspan", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN", - "Galaxy wrapper version": "0.4", - "Conda id": "graphclust-wrappers", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "agat", - "Galaxy tool ids": [ - "agat" - ], - "Description": "GTF/GFF analysis toolkit", - "bio.tool id": "agat", - "bio.tool ids": [ - "agat" - ], - "biii": null, - "bio.tool name": "AGAT", - "bio.tool description": "Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.", - "EDAM operation": [ - "Data handling", - "Genome annotation" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/NBISweden/AGAT", - "ToolShed categories": [ - "Convert Formats", - "Statistics", - "Fasta Manipulation" - ], - "ToolShed id": "agat", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", - "Galaxy wrapper version": "1.2.0", - "Conda id": "agat", - "Conda version": "1.4.0", - "EDAM operation (no superclasses)": [ - "Data handling", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "antismash", - "Galaxy tool ids": [ - "antismash" - ], - "Description": "Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters", - "bio.tool id": "antismash", - "bio.tool ids": [ - "antismash" - ], - "biii": null, - "bio.tool name": "antiSMASH", - "bio.tool description": "Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.", - "EDAM operation": [ - "Sequence clustering", - "Gene prediction", - "Differential gene expression analysis" - ], - "EDAM topic": [ - "Molecular interactions, pathways and networks", - "Gene and protein families" - ], - "Status": "To update", - "Source": "https://antismash.secondarymetabolites.org", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "antismash", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/antismash", - "Galaxy wrapper version": "6.1.1", - "Conda id": "antismash", - "Conda version": "7.1.0", - "EDAM operation (no superclasses)": [ - "Sequence clustering", - "Gene prediction", - "Differential gene expression analysis" - ], - "EDAM topic (no superclasses)": [ - "Molecular interactions, pathways and networks", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "atactk_trim_adapters", - "Galaxy tool ids": [ - "atactk_trim_adapters" - ], - "Description": "Trim adapters from paired-end HTS reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ParkerLab/atactk/", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "atactk_trim_adapters", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters", - "Galaxy wrapper version": "0.1.6", - "Conda id": "atactk", - "Conda version": "0.1.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "augustus", - "Galaxy tool ids": [ - "augustus" - ], - "Description": "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bioinf.uni-greifswald.de/augustus/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "augustus", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/augustus", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/augustus", - "Galaxy wrapper version": "3.1.0", - "Conda id": "augustus", - "Conda version": "3.5.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bamhash", - "Galaxy tool ids": [ - "bamhash" - ], - "Description": "Hash BAM and FASTQ files to verify data integrity", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/DecodeGenetics/BamHash", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bamhash", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bamhash", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bamhash", - "Galaxy wrapper version": "1.1", - "Conda id": "bamhash", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "barcode_collapse", - "Galaxy tool ids": [ - "barcode_collapse" - ], - "Description": "Paired End randomer aware duplicate removal algorithm", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/YeoLab/gscripts", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "barcode_collapse", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse", - "Galaxy wrapper version": "0.1.0", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bigwig_to_bedgraph", - "Galaxy tool ids": [ - "bigwig_to_bedgraph" - ], - "Description": "Convert from bigWig to bedGraph format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "bigwig_to_bedgraph", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph", - "Galaxy wrapper version": "0.1.0", - "Conda id": "ucsc_tools", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biomodelsML", - "Galaxy tool ids": [ - "biomodels_biomd0000001066", - "biomodels_biomd0000001076" - ], - "Description": "Wrappers for tools to bring BioModels AI models into Galaxy.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ebi.ac.uk/biomodels/", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "biomodels", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML", - "Galaxy wrapper version": "1.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bionano", - "Galaxy tool ids": [ - "bionano_scaffold" - ], - "Description": "Bionano Solve is a set of tools for analyzing Bionano data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bionanogenomics.com/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "bionano", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bionano", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bionano", - "Galaxy wrapper version": "3.7.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bismark", - "Galaxy tool ids": [ - "bismark_pretty_report", - "bismark_bowtie2", - "bismark_deduplicate", - "bismark_methylation_extractor" - ], - "Description": "A tool to map bisulfite converted sequence reads and determine cytosine methylation states", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.bioinformatics.babraham.ac.uk/projects/bismark/", - "ToolShed categories": [ - "Sequence Analysis", - "Next Gen Mappers" - ], - "ToolShed id": "bismark", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bismark", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bismark", - "Galaxy wrapper version": "0.22.1", - "Conda id": "bismark", - "Conda version": "0.24.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "blobtoolkit", - "Galaxy tool ids": [ - "blobtoolkit" - ], - "Description": "Identification and isolation non-target data in draft and publicly available genome assemblies.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://blobtoolkit.genomehubs.org/", - "ToolShed categories": [ - "Sequence Analysis", - "Assembly" - ], - "ToolShed id": "blobtoolkit", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit", - "Galaxy wrapper version": "4.0.7", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blockbuster", - "Galaxy tool ids": [ - "blockbuster" - ], - "Description": "Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "blockbuster", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster", - "Galaxy wrapper version": "0.1.2", - "Conda id": "blockbuster", - "Conda version": "0.0.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "canu", - "Galaxy tool ids": [ - "canu" - ], - "Description": "Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).", - "bio.tool id": "canu", - "bio.tool ids": [ - "canu" - ], - "biii": null, - "bio.tool name": "CANU", - "bio.tool description": "De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.", - "EDAM operation": [ - "De-novo assembly" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/canu", - "ToolShed categories": [], - "ToolShed id": "canu", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/canu", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/canu", - "Galaxy wrapper version": "2.2", - "Conda id": "canu", - "Conda version": "2.2", - "EDAM operation (no superclasses)": [ - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cellpose", - "Galaxy tool ids": [ - "cellpose" - ], - "Description": "Cellpose is an anatomical segmentation algorithm", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/MouseLand/cellpose", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "cellpose", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/cellpose", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellpose", - "Galaxy wrapper version": "3.0.8", - "Conda id": "cellpose", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cellprofiler", - "Galaxy tool ids": [ - "cp_cellprofiler", - "cp_color_to_gray", - "cp_convert_objects_to_image", - "cp_display_data_on_image", - "cp_enhance_or_suppress_features", - "cp_export_to_spreadsheet", - "cp_gray_to_color", - "cp_identify_primary_objects", - "cp_image_math", - "cp_mask_image", - "cp_measure_granularity", - "cp_measure_image_area_occupied", - "cp_measure_image_intensity", - "cp_measure_image_quality", - "cp_measure_object_intensity", - "cp_measure_object_size_shape", - "cp_measure_texture", - "cp_overlay_outlines", - "cp_relate_objects", - "cp_save_images", - "cp_common", - "cp_tile", - "cp_track_objects" - ], - "Description": "cellProfiler wrapper", - "bio.tool id": "CellProfiler", - "bio.tool ids": [ - "CellProfiler" - ], - "biii": "cellprofiler", - "bio.tool name": "CellProfiler", - "bio.tool description": "Tool for quantifying data from biological images, particularly in high-throughput experiments.", - "EDAM operation": [ - "Quantification", - "Image analysis", - "Parsing" - ], - "EDAM topic": [ - "Imaging", - "Microarray experiment", - "Genotype and phenotype" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "cellprofiler", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Quantification", - "Image analysis", - "Parsing" - ], - "EDAM topic (no superclasses)": [ - "Imaging", - "Microarray experiment", - "Genotype and phenotype" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 23, - "Available on UseGalaxy.eu": 23, - "Available on UseGalaxy.org.fr": 19 - }, - { - "Galaxy wrapper id": "cellprofiler_v4", - "Galaxy tool ids": [ - "cp_cellprofiler4" - ], - "Description": "cellProfiler4 wrapper", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "cellprofiler4", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4", - "Galaxy wrapper version": "4.2.6", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "chipseeker", - "Galaxy tool ids": [ - "chipseeker" - ], - "Description": "A tool for ChIP peak annotation and visualization", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html", - "ToolShed categories": [ - "ChIP-seq", - "Genome annotation" - ], - "ToolShed id": "chipseeker", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker", - "Galaxy wrapper version": "1.32.0", - "Conda id": "bioconductor-chipseeker", - "Conda version": "1.38.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "circexplorer", - "Galaxy tool ids": [ - "circexplorer" - ], - "Description": "A combined strategy to identify circular RNAs (circRNAs and ciRNAs)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/YangLab/CIRCexplorer", - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "circexplorer", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer", - "Galaxy wrapper version": "1.1.9.0", - "Conda id": "circexplorer", - "Conda version": "1.1.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "combine_metaphlan_humann", - "Galaxy tool ids": [ - "combine_metaphlan_humann" - ], - "Description": "Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances", - "bio.tool id": "combine_metaphlan_and_humann", - "bio.tool ids": [ - "combine_metaphlan_and_humann" - ], - "biii": null, - "bio.tool name": "Combine Metaphlan and HUMAnN", - "bio.tool description": "This tool combine MetaPhlAn outputs and HUMANnN outputs", - "EDAM operation": [ - "Aggregation" - ], - "EDAM topic": [ - "Metagenomics", - "Molecular interactions, pathways and networks" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "combine_metaphlan2_humann2", - "Galaxy wrapper owner": "bebatut", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann", - "Galaxy wrapper version": "0.3.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Aggregation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Molecular interactions, pathways and networks" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "compare_humann2_output", - "Galaxy tool ids": [ - "compare_humann2_output" - ], - "Description": "Compare outputs of HUMAnN2 for several samples and extract similar and specific information", - "bio.tool id": "compare_humann2_outputs", - "bio.tool ids": [ - "compare_humann2_outputs" - ], - "biii": null, - "bio.tool name": "Compare HUMAnN2 outputs", - "bio.tool description": "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples", - "EDAM operation": [ - "Comparison" - ], - "EDAM topic": [ - "Metagenomics", - "Gene and protein families" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "compare_humann2_output", - "Galaxy wrapper owner": "bebatut", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output", - "Galaxy wrapper version": "0.2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Comparison" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cpat", - "Galaxy tool ids": [ - "cpat" - ], - "Description": "Coding-potential assessment tool using an alignment-free logistic regression model.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/liguowang/cpat", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cpat", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/cpat", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cpat", - "Galaxy wrapper version": "3.0.5", - "Conda id": "cpat", - "Conda version": "3.0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "crt", - "Galaxy tool ids": [ - "crispr_recognition_tool" - ], - "Description": "CRISPR Recognition Tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "crispr_recognition_tool", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/crt", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/crt", - "Galaxy wrapper version": "1.2.0", - "Conda id": "crisper_recognition_tool", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "diff", - "Galaxy tool ids": [ - "diff" - ], - "Description": "GNU diff tool that calculates the differences between two files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.gnu.org/software/diffutils/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "diff", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/diff", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/diff", - "Galaxy wrapper version": "3.7", - "Conda id": "diffutils", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "diffbind", - "Galaxy tool ids": [], - "Description": "Diffbind provides functions for processing ChIP-Seq data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bioconductor.org/packages/release/bioc/html/DiffBind.html", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "diffbind", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/diffbind", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/diffbind", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "edta", - "Galaxy tool ids": [ - "edta" - ], - "Description": "The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. ", - "bio.tool id": "edta", - "bio.tool ids": [ - "edta" - ], - "biii": null, - "bio.tool name": "The Extensive de novo TE Annotator (EDTA)", - "bio.tool description": "The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.", - "EDAM operation": [ - "De-novo assembly", - "Deisotoping", - "Genome annotation" - ], - "EDAM topic": [ - "Workflows", - "Mobile genetic elements", - "Plant biology", - "Transcription factors and regulatory sites", - "Model organisms" - ], - "Status": "To update", - "Source": "https://github.com/oushujun/EDTA", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "edta", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/edta", - "Galaxy wrapper version": null, - "Conda id": "edta", - "Conda version": "2.2.0", - "EDAM operation (no superclasses)": [ - "De-novo assembly", - "Deisotoping", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Workflows", - "Mobile genetic elements", - "Plant biology", - "Transcription factors and regulatory sites", - "Model organisms" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "epicseg", - "Galaxy tool ids": [ - "epicseg_segment" - ], - "Description": "EpiCSeg is a tool for conducting chromatin segmentation.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/lamortenera/epicseg", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "epicseg", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/epicseg", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/epicseg", - "Galaxy wrapper version": "@VERSION_STRING@", - "Conda id": "epicseg", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_info", - "Galaxy tool ids": [ - "fastq_info" - ], - "Description": "FASTQ info allows to validate single or paired fastq files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nunofonseca/fastq_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_info", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info", - "Galaxy wrapper version": "0.25.1", - "Conda id": "fastq_utils", - "Conda version": "0.25.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "file_manipulation", - "Galaxy tool ids": [ - "bg_uniq" - ], - "Description": "This tool returns all unique lines from a tab-separated file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "unique", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", - "Galaxy wrapper version": "0.4", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "find_subsequences", - "Galaxy tool ids": [ - "bg_find_subsequences" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "find_subsequences", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences", - "Galaxy wrapper version": "0.3", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "flye", - "Galaxy tool ids": [ - "flye" - ], - "Description": "Assembly of long and error-prone reads.", - "bio.tool id": "Flye", - "bio.tool ids": [ - "Flye" - ], - "biii": null, - "bio.tool name": "Flye", - "bio.tool description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.", - "EDAM operation": [ - "Genome assembly", - "De-novo assembly", - "Mapping assembly", - "Cross-assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Metagenomics", - "Whole genome sequencing", - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/fenderglass/Flye/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "flye", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/flye", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/flye", - "Galaxy wrapper version": "2.9.3", - "Conda id": "flye", - "Conda version": "2.9.4", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "De-novo assembly", - "Mapping assembly", - "Cross-assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Metagenomics", - "Whole genome sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "footprint", - "Galaxy tool ids": [ - "footprint" - ], - "Description": "Find transcription factor footprints", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "footprint", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/footprint", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/footprint", - "Galaxy wrapper version": "1.0.0", - "Conda id": "footprint", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "format_cd_hit_output", - "Galaxy tool ids": [ - "format_cd_hit_output" - ], - "Description": "Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "format_cd_hit_output", - "Galaxy wrapper owner": "bebatut", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output", - "Galaxy wrapper version": "1.0.0+galaxy1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "format_metaphlan2_output", - "Galaxy tool ids": [ - "format_metaphlan2_output" - ], - "Description": "Format MetaPhlAn2 output to extract abundance at different taxonomic levels", - "bio.tool id": "format_metaphlan2_output", - "bio.tool ids": [ - "format_metaphlan2_output" - ], - "biii": null, - "bio.tool name": "Format metaphlan2 output", - "bio.tool description": "This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).", - "EDAM operation": [ - "Formatting" - ], - "EDAM topic": [ - "Taxonomy", - "Metagenomics" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "format_metaphlan2_output", - "Galaxy wrapper owner": "bebatut", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output", - "Galaxy wrapper version": "0.2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Formatting" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gfastats", - "Galaxy tool ids": [ - "gfastats" - ], - "Description": "Tool for generating sequence statistics and simultaneous genome assembly file manipulation.", - "bio.tool id": "gfastats", - "bio.tool ids": [ - "gfastats" - ], - "biii": null, - "bio.tool name": "gfastats", - "bio.tool description": "gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.", - "EDAM operation": [ - "Data handling" - ], - "EDAM topic": [ - "Computational biology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/vgl-hub/gfastats", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gfastats", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/gfastats", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/gfastats", - "Galaxy wrapper version": "1.3.6", - "Conda id": "gfastats", - "Conda version": "1.3.6", - "EDAM operation (no superclasses)": [ - "Data handling" - ], - "EDAM topic (no superclasses)": [ - "Computational biology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "glimmer_hmm", - "Galaxy tool ids": [], - "Description": "GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://ccb.jhu.edu/software/glimmerhmm/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "glimmer_hmm", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gotohscan", - "Galaxy tool ids": [ - "rbc_gotohscan" - ], - "Description": "Find subsequences in db", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gotohscan", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan", - "Galaxy wrapper version": "1.3.0", - "Conda id": "gotohscan", - "Conda version": "1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graph_converter", - "Galaxy tool ids": [ - "graph_converter" - ], - "Description": "Convert between different graph formats", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "graph_converter", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter", - "Galaxy wrapper version": "0.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphclust", - "Galaxy tool ids": [ - "graphclust" - ], - "Description": "GraphClust can be used for structural clustering of RNA sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.bioinf.uni-freiburg.de/Software/GraphClust/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "graphclust", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graphclust", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graphclust", - "Galaxy wrapper version": "0.1", - "Conda id": "GraphClust", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphmap", - "Galaxy tool ids": [ - "graphmap_align", - "graphmap_overlap" - ], - "Description": "Mapper for long, error-prone reads.", - "bio.tool id": "graphmap", - "bio.tool ids": [ - "graphmap" - ], - "biii": null, - "bio.tool name": "graphmap", - "bio.tool description": "Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1", - "EDAM operation": [ - "Sequence trimming", - "EST assembly", - "Read mapping" - ], - "EDAM topic": [ - "Gene transcripts", - "RNA-Seq", - "RNA splicing" - ], - "Status": "To update", - "Source": "https://github.com/isovic/graphmap/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "graphmap", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graphmap", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graphmap", - "Galaxy wrapper version": "0.5.2", - "Conda id": "graphmap", - "Conda version": "0.6.3", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "EST assembly", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Gene transcripts", - "RNA-Seq", - "RNA splicing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hclust2", - "Galaxy tool ids": [ - "hclust2" - ], - "Description": "Plots heatmaps", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/nsegata/hclust2/", - "ToolShed categories": [ - "Data Visualization" - ], - "ToolShed id": "hclust2", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hclust2", - "Galaxy wrapper version": "0.99", - "Conda id": "hclust2", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hictk", - "Galaxy tool ids": [ - "hictk" - ], - "Description": "Convert cooler to juicebox_hic", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/paulsengroup/hictk", - "ToolShed categories": [ - "Convert Formats", - "Epigenetics" - ], - "ToolShed id": "hictk", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hictk", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hictk", - "Galaxy wrapper version": "0.0.12", - "Conda id": "hictk", - "Conda version": "0.0.12", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hicup", - "Galaxy tool ids": [ - "hicup2juicer", - "hicup_deduplicator", - "hicup_digester", - "hicup_filter", - "hicup_hicup", - "hicup_mapper", - "hicup_truncater" - ], - "Description": "The HiCUP-Pipeline from the Bioinformatics Babraham Institute.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "hicup", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hicup", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hicup", - "Galaxy wrapper version": "0.9.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 7, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hifiasm", - "Galaxy tool ids": [ - "hifiasm" - ], - "Description": "A fast haplotype-resolved de novo assembler", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/chhylp123/hifiasm", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hifiasm", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm", - "Galaxy wrapper version": "0.19.8", - "Conda id": "hifiasm", - "Conda version": "0.19.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "homer", - "Galaxy tool ids": [], - "Description": "Software for motif discovery and next generation sequencing analysis.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://homer.salk.edu/homer/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "homer", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/homer", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/homer", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "illumina_methylation_analyser", - "Galaxy tool ids": [ - "illumina_methylation_analyser" - ], - "Description": "Methylation analyzer for Illumina 450k DNA emthylation microarrays", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "illumina_methylation_analyser", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", - "Galaxy wrapper version": "0.1", - "Conda id": "Rscript", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bia-ftplinks", - "Galaxy tool ids": [ - "bia_download" - ], - "Description": "Tool to query ftp links for study from bioimage archive", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "bia_download", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks", - "Galaxy wrapper version": "0.1.0", - "Conda id": "wget", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphicsmagick", - "Galaxy tool ids": [ - "graphicsmagick_image_compare", - "graphicsmagick_image_convert", - "graphicsmagick_image_montage" - ], - "Description": "Contains tools based on GraphicsMagick", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.graphicsmagick.org", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "graphicsmagick", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick", - "Galaxy wrapper version": "1.3.43", - "Conda id": "graphicsmagick", - "Conda version": "1.3.26", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "imagej2", - "Galaxy tool ids": [ - "imagej2_adjust_threshold_binary", - "imagej2_analyze_particles_binary", - "imagej2_analyze_skeleton", - "imagej2_binary_to_edm", - "imagej2_bunwarpj_adapt_transform", - "imagej2_bunwarpj_align", - "imagej2_bunwarpj_compare_elastic", - "imagej2_bunwarpj_compare_elastic_raw", - "imagej2_bunwarpj_compare_raw", - "imagej2_bunwarpj_compose_elastic", - "imagej2_bunwarpj_compose_raw", - "imagej2_bunwarpj_compose_raw_elastic", - "imagej2_bunwarpj_convert_to_raw", - "imagej2_bunwarpj_elastic_transform", - "imagej2_bunwarpj_raw_transform", - "imagej2_create_image", - "imagej2_enhance_contrast", - "imagej2_find_edges", - "imagej2_find_maxima", - "imagej2_make_binary", - "imagej2_math", - "imagej2_noise", - "imagej2_shadows", - "imagej2_sharpen", - "imagej2_skeletonize3d", - "imagej2_smooth", - "imagej2_watershed_binary" - ], - "Description": "ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.", - "bio.tool id": "imagej", - "bio.tool ids": [ - "imagej" - ], - "biii": "imagej2", - "bio.tool name": "ImageJ2", - "bio.tool description": "It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.", - "EDAM operation": [ - "Image analysis", - "Image annotation", - "Visualisation" - ], - "EDAM topic": [ - "Imaging" - ], - "Status": "To update", - "Source": "http://fiji.sc", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "imagej2", - "Galaxy wrapper owner": "imgteam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Image analysis", - "Image annotation", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Imaging" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 27, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "woundhealing", - "Galaxy tool ids": [ - "woundhealing_scratch_assay" - ], - "Description": "Tool to automate quantification of wound healing in high-throughput microscopy scratch assays", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://git.embl.de/grp-cba/wound-healing-htm-screen", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "Wound healing scratch assay image analysis", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing", - "Galaxy wrapper version": "1.6.1", - "Conda id": "fiji-morpholibj", - "Conda version": "1.6.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "instagraal", - "Galaxy tool ids": [ - "instagraal" - ], - "Description": "Large genome reassembly based on Hi-C data", - "bio.tool id": "instagraal", - "bio.tool ids": [ - "instagraal" - ], - "biii": null, - "bio.tool name": "instaGRAAL", - "bio.tool description": "Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)", - "EDAM operation": [ - "Genome assembly", - "Mapping assembly", - "Genetic mapping", - "Scaffolding" - ], - "EDAM topic": [ - "Sequence assembly", - "Mapping", - "Metagenomics", - "Statistics and probability", - "DNA binding sites" - ], - "Status": "To update", - "Source": "https://github.com/koszullab/instaGRAAL", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "instagraal", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/instagraal", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/instagraal", - "Galaxy wrapper version": "0.1.6", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Mapping assembly", - "Genetic mapping", - "Scaffolding" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Mapping", - "Metagenomics", - "Statistics and probability", - "DNA binding sites" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "iprscan5", - "Galaxy tool ids": [], - "Description": "Interproscan queries the interpro database and provides annotations.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.ebi.ac.uk/Tools/pfa/iprscan5/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "iprscan5", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "itsx", - "Galaxy tool ids": [ - "itsx" - ], - "Description": "ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.", - "bio.tool id": "ITSx", - "bio.tool ids": [ - "ITSx" - ], - "biii": null, - "bio.tool name": "ITSx", - "bio.tool description": "TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.", - "EDAM operation": [ - "Sequence feature detection" - ], - "EDAM topic": [ - "Functional, regulatory and non-coding RNA", - "Microbiology" - ], - "Status": "Up-to-date", - "Source": "https://microbiology.se/software/itsx/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "itsx", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/itsx", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/itsx", - "Galaxy wrapper version": "1.1.3", - "Conda id": "itsx", - "Conda version": "1.1.3", - "EDAM operation (no superclasses)": [ - "Sequence feature detection" - ], - "EDAM topic (no superclasses)": [ - "Functional, regulatory and non-coding RNA", - "Microbiology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "jbrowse2", - "Galaxy tool ids": [ - "jbrowse2" - ], - "Description": "JBrowse2 Genome Browser integrated as a Galaxy Tool", - "bio.tool id": "jbrowse2", - "bio.tool ids": [ - "jbrowse2" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://jbrowse.org", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "jbrowse2", - "Galaxy wrapper owner": "fubar", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2", - "Galaxy wrapper version": "2.11.1", - "Conda id": "jbrowse2", - "Conda version": "2.11.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "jupyter_job", - "Galaxy tool ids": [ - "run_jupyter_job" - ], - "Description": "Run jupyter notebook script in Galaxy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "run_jupyter_job", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job", - "Galaxy wrapper version": "0.0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "labels", - "Galaxy tool ids": [ - "bg_labels" - ], - "Description": "remaps and annotates alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "labels", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", - "Galaxy wrapper version": "1.0.5.0", - "Conda id": "labels", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lighter", - "Galaxy tool ids": [ - "lighter" - ], - "Description": "Lighter is a kmer-based error correction method for whole genome sequencing data", - "bio.tool id": "lighter", - "bio.tool ids": [ - "lighter" - ], - "biii": null, - "bio.tool name": "Lighter", - "bio.tool description": "Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.", - "EDAM operation": [ - "k-mer counting", - "Sequence read processing", - "Sequencing quality control", - "Sequencing error detection" - ], - "EDAM topic": [ - "Sequencing", - "Whole genome sequencing", - "DNA", - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/mourisl/Lighter", - "ToolShed categories": [ - "Sequence Analysis", - "Fasta Manipulation" - ], - "ToolShed id": "lighter", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/lighter", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/lighter", - "Galaxy wrapper version": "1.0", - "Conda id": "lighter", - "Conda version": "1.1.3", - "EDAM operation (no superclasses)": [ - "k-mer counting", - "Sequence read processing", - "Sequencing quality control", - "Sequencing error detection" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "DNA", - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mafft", - "Galaxy tool ids": [ - "rbc_mafft_add", - "rbc_mafft" - ], - "Description": "Multiple alignment program for amino acid or nucleotide sequences", - "bio.tool id": "MAFFT", - "bio.tool ids": [ - "MAFFT" - ], - "biii": null, - "bio.tool name": "MAFFT", - "bio.tool description": "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.", - "EDAM operation": [ - "Multiple sequence alignment" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://mafft.cbrc.jp/alignment/software/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "mafft", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mafft", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mafft", - "Galaxy wrapper version": "7.520", - "Conda id": "mafft", - "Conda version": "7.525", - "EDAM operation (no superclasses)": [ - "Multiple sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "mavedb", - "Galaxy tool ids": [ - "mavedb_importer" - ], - "Description": "data source for MaveDB", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "mavedb_importer", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb", - "Galaxy wrapper version": "0.9", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "methtools", - "Galaxy tool ids": [ - "methtools_calling", - "r_correlation_matrix", - "methtools_destrand", - "methtools_dmr", - "methtools_filter", - "methtools_plot", - "smooth_running_window", - "methtools_tiling" - ], - "Description": "tools for methylation analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "methtools", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", - "Galaxy wrapper version": "0.1.1", - "Conda id": "methtools", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "methyldackel", - "Galaxy tool ids": [ - "pileometh" - ], - "Description": "A tool for processing bisulfite sequencing alignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/dpryan79/MethylDackel", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pileometh", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel", - "Galaxy wrapper version": "0.5.2", - "Conda id": "methyldackel", - "Conda version": "0.6.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "methylkit", - "Galaxy tool ids": [ - "methylkit" - ], - "Description": "A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bioconductor.org/packages/release/bioc/html/methylKit.html", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "methylkit", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methylkit", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methylkit", - "Galaxy wrapper version": "0.99.2", - "Conda id": "bioconductor-methylkit", - "Conda version": "1.28.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "metilene", - "Galaxy tool ids": [ - "metilene" - ], - "Description": "Differential DNA methylation calling", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA", - "Statistics" - ], - "ToolShed id": "metilene", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/metilene", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/metilene", - "Galaxy wrapper version": "0.2.6.1", - "Conda id": "metilene", - "Conda version": "0.2.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "mgnify_seqprep", - "Galaxy tool ids": [ - "mgnify_seqprep" - ], - "Description": "A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.", - "bio.tool id": "seqprep", - "bio.tool ids": [ - "seqprep" - ], - "biii": null, - "bio.tool name": "SeqPrep", - "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", - "EDAM operation": [ - "Nucleic acid design" - ], - "EDAM topic": [ - "Genomics", - "Sequence assembly", - "Sequencing", - "Probes and primers" - ], - "Status": "To update", - "Source": "https://github.com/jstjohn/SeqPrep", - "ToolShed categories": [ - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "mgnify_seqprep", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep", - "Galaxy wrapper version": "1.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Nucleic acid design" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly", - "Sequencing", - "Probes and primers" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "miclip", - "Galaxy tool ids": [ - "mi_clip" - ], - "Description": "Identification of binding sites in CLIP-Seq data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cran.r-project.org/src/contrib/Archive/MiClip/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "miclip", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/miclip", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/miclip", - "Galaxy wrapper version": "1.2.0", - "Conda id": "Rscript", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "minced", - "Galaxy tool ids": [ - "minced" - ], - "Description": "MinCED - Mining CRISPRs in Environmental Datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "minced", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/minced", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/minced", - "Galaxy wrapper version": "0.2.0", - "Conda id": "minced", - "Conda version": "0.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "minipolish", - "Galaxy tool ids": [ - "minipolish" - ], - "Description": "Polishing miniasm assemblies", - "bio.tool id": "minipolish", - "bio.tool ids": [ - "minipolish" - ], - "biii": null, - "bio.tool name": "minipolish", - "bio.tool description": "A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.", - "EDAM operation": [ - "Localised reassembly", - "Read depth analysis" - ], - "EDAM topic": [ - "Sequence assembly", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/rrwick/Minipolish", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "minipolish", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/minipolish", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/minipolish", - "Galaxy wrapper version": "0.1.3", - "Conda id": "minipolish", - "Conda version": "0.1.3", - "EDAM operation (no superclasses)": [ - "Localised reassembly", - "Read depth analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mitohifi", - "Galaxy tool ids": [ - "mitohifi" - ], - "Description": "Assembly mitogenomes from Pacbio HiFi read.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "mitohifi", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi", - "Galaxy wrapper version": "3", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "molecule2gspan", - "Galaxy tool ids": [ - "bg_mol2gspan" - ], - "Description": "converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "molecule_to_gspan", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", - "Galaxy wrapper version": "0.2", - "Conda id": "openbabel", - "Conda version": "2.3.90dev7d621d9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "music_deconvolution", - "Galaxy tool ids": [ - "music_construct_eset", - "music_inspect_eset", - "music_manipulate_eset", - "music_compare", - "music_deconvolution" - ], - "Description": "Multi-subject Single Cell deconvolution (MuSiC)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/xuranw/MuSiC", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "music", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution", - "Galaxy wrapper version": "0.1.1", - "Conda id": "music-deconvolution", - "Conda version": "0.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nanopolish", - "Galaxy tool ids": [ - "nanopolish_eventalign", - "nanopolish_methylation", - "nanopolish_polya", - "nanopolish_variants" - ], - "Description": "Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/jts/nanopolish", - "ToolShed categories": [], - "ToolShed id": "nanopolish", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish", - "Galaxy wrapper version": "0.14.0", - "Conda id": "nanopolish", - "Conda version": "0.14.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "netboxr", - "Galaxy tool ids": [ - "netboxr" - ], - "Description": "netboxr enables automated discovery of biological process modules by network analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Systems Biology" - ], - "ToolShed id": "netboxr", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/netboxr", - "Galaxy wrapper version": "1.6.0", - "Conda id": "bioconductor-netboxr", - "Conda version": "1.9.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nextdenovo", - "Galaxy tool ids": [ - "nextdenovo" - ], - "Description": "String graph-based de novo assembler for long reads", - "bio.tool id": "nextdenovo", - "bio.tool ids": [ - "nextdenovo" - ], - "biii": null, - "bio.tool name": "NextDenovo", - "bio.tool description": "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a \"correct-then-assemble\" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.", - "EDAM operation": [ - "De-novo assembly", - "Genome assembly" - ], - "EDAM topic": [ - "Sequencing", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/Nextomics/NextDenovo", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "nextdenovo", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo", - "Galaxy wrapper version": "2.5.0", - "Conda id": "nextdenovo", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "De-novo assembly", - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nucleosome_prediction", - "Galaxy tool ids": [ - "Nucleosome" - ], - "Description": "Prediction of Nucleosomes Positions on the Genome", - "bio.tool id": "nucleosome_prediction", - "bio.tool ids": [ - "nucleosome_prediction" - ], - "biii": null, - "bio.tool name": "nucleosome_prediction", - "bio.tool description": "Prediction of Nucleosomes Positions on the Genome", - "EDAM operation": [ - "Prediction and recognition", - "Nucleosome position prediction", - "Sequence analysis" - ], - "EDAM topic": [ - "Structural genomics", - "Nucleic acid sites, features and motifs" - ], - "Status": "Up-to-date", - "Source": "https://genie.weizmann.ac.il/software/nucleo_exe.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "nucleosome_prediction", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction", - "Galaxy wrapper version": "3.0", - "Conda id": "nucleosome_prediction", - "Conda version": "3.0", - "EDAM operation (no superclasses)": [ - "Prediction and recognition", - "Nucleosome position prediction", - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Structural genomics", - "Nucleic acid sites, features and motifs" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "numeric_clustering", - "Galaxy tool ids": [ - "numeric_clustering" - ], - "Description": "Clustering tool for numberic values", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://scikit-learn.org/stable/index.html", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "numeric_clustering", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering", - "Galaxy wrapper version": "0.9", - "Conda id": "anaconda", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "openms", - "Galaxy tool ids": [ - "AccurateMassSearch", - "AdditiveSeries", - "BaselineFilter", - "CVInspector", - "CompNovo", - "CompNovoCID", - "ConsensusID", - "ConsensusMapNormalizer", - "ConvertTSVToTraML", - "ConvertTraMLToTSV", - "DTAExtractor", - "DeMeanderize", - "Decharger", - "DecoyDatabase", - "Digestor", - "DigestorMotif", - "EICExtractor", - "ERPairFinder", - "ExternalCalibration", - "FFEval", - "FalseDiscoveryRate", - "FeatureFinderCentroided", - "FeatureFinderIdentification", - "FeatureFinderIsotopeWavelet", - "FeatureFinderMRM", - "FeatureFinderMetabo", - "FeatureFinderMultiplex", - "FeatureFinderSuperHirn", - "FeatureLinkerLabeled", - "FeatureLinkerUnlabeled", - "FeatureLinkerUnlabeledQT", - "FidoAdapter", - "FileConverter", - "FileFilter", - "FileInfo", - "FileMerger", - "FuzzyDiff", - "HighResPrecursorMassCorrector", - "IDConflictResolver", - "IDDecoyProbability", - "IDExtractor", - "IDFileConverter", - "IDFilter", - "IDMapper", - "IDMassAccuracy", - "IDMerger", - "IDPosteriorErrorProbability", - "IDRTCalibration", - "IDRipper", - "IDScoreSwitcher", - "IDSplitter", - "ITRAQAnalyzer", - "InclusionExclusionListCreator", - "InspectAdapter", - "InternalCalibration", - "IsobaricAnalyzer", - "LabeledEval", - "LowMemPeakPickerHiRes", - "LowMemPeakPickerHiRes_RandomAccess", - "LuciphorAdapter", - "MRMMapper", - "MRMPairFinder", - "MRMTransitionGroupPicker", - "MSGFPlusAdapter", - "MSSimulator", - "MapAlignmentEvaluation", - "MapNormalizer", - "MapRTTransformer", - "MapStatistics", - "MascotAdapter", - "MascotAdapterOnline", - "MassCalculator", - "MassTraceExtractor", - "MetaProSIP", - "MetaboliteSpectralMatcher", - "MultiplexResolver", - "MzMLSplitter", - "MzTabExporter", - "NoiseFilterGaussian", - "NoiseFilterSGolay", - "OpenSwathAnalyzer", - "OpenSwathAssayGenerator", - "OpenSwathChromatogramExtractor", - "OpenSwathConfidenceScoring", - "OpenSwathDIAPreScoring", - "OpenSwathDecoyGenerator", - "OpenSwathFeatureXMLToTSV", - "OpenSwathFileSplitter", - "OpenSwathMzMLFileCacher", - "OpenSwathRTNormalizer", - "OpenSwathRewriteToFeatureXML", - "OpenSwathWorkflow", - "PTModel", - "PTPredict", - "PeakPickerHiRes", - "PeakPickerIterative", - "PeakPickerWavelet", - "PepNovoAdapter", - "PeptideIndexer", - "PhosphoScoring", - "PrecursorIonSelector", - "PrecursorMassCorrector", - "ProteinInference", - "ProteinQuantifier", - "ProteinResolver", - "QCCalculator", - "QCEmbedder", - "QCExporter", - "QCExtractor", - "QCImporter", - "QCMerger", - "QCShrinker", - "RNPxl", - "RNPxlXICFilter", - "RTEvaluation", - "RTModel", - "RTPredict", - "SemanticValidator", - "SequenceCoverageCalculator", - "SimpleSearchEngine", - "SpecLibCreator", - "SpectraFilterBernNorm", - "SpectraFilterMarkerMower", - "SpectraFilterNLargest", - "SpectraFilterNormalizer", - "SpectraFilterParentPeakMower", - "SpectraFilterScaler", - "SpectraFilterSqrtMower", - "SpectraFilterThresholdMower", - "SpectraFilterWindowMower", - "SpectraMerger", - "SvmTheoreticalSpectrumGeneratorTrainer", - "TICCalculator", - "TMTAnalyzer", - "TOFCalibration", - "TextExporter", - "TopPerc", - "TransformationEvaluation", - "XMLValidator", - "XTandemAdapter" - ], - "Description": "OpenMS in version 2.1.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "openms", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/openms", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/openms", - "Galaxy wrapper version": "2.1.0", - "Conda id": "openms", - "Conda version": "3.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 7, - "Available on UseGalaxy.org.au": 34, - "Available on UseGalaxy.eu": 135, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pandas_rolling_window", - "Galaxy tool ids": [ - "pandas_rolling_window" - ], - "Description": "Rolling window calculations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "pandas_rolling_window", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window", - "Galaxy wrapper version": "0.1", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "peakachu", - "Galaxy tool ids": [ - "peakachu" - ], - "Description": "PEAKachu is a peak-caller for CLIP- and RIP-Seq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "peakachu", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/tbischler/PEAKachu", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/peakachu", - "Galaxy wrapper version": "0.2.0+galaxy1", - "Conda id": "peakachu", - "Conda version": "0.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "perf", - "Galaxy tool ids": [ - "stats_perf_tool" - ], - "Description": "suitable for boolean classification problems", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://osmot.cs.cornell.edu/kddcup/software.html", - "ToolShed categories": [], - "ToolShed id": "stats_perf_tool", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/perf", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/perf", - "Galaxy wrapper version": "5.11.0", - "Conda id": "perf", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pfamscan", - "Galaxy tool ids": [ - "pfamscan" - ], - "Description": "Search a FASTA sequence against a library of Pfam HMM.", - "bio.tool id": "pfamscan", - "bio.tool ids": [ - "pfamscan" - ], - "biii": null, - "bio.tool name": "PfamScan", - "bio.tool description": "This tool is used to search a FASTA sequence against a library of Pfam HMM.", - "EDAM operation": [ - "Protein sequence analysis" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pfamscan", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan", - "Galaxy wrapper version": "1.6", - "Conda id": "pfam_scan", - "Conda version": "1.6", - "EDAM operation (no superclasses)": [ - "Protein sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pg_tools", - "Galaxy tool ids": [ - "pg_dump", - "pg_import", - "pg_query" - ], - "Description": "tool suite for dealing with Postgresql databases from Galaxy's history", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.postgresql.org", - "ToolShed categories": [ - "Data Export", - "Data Source" - ], - "ToolShed id": "pgtools", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/pgtools", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools", - "Galaxy wrapper version": null, - "Conda id": "postgresql", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pharmcat", - "Galaxy tool ids": [ - "pharmcat" - ], - "Description": "Pharmacogenomics Clinical Annotation Tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pharmcat.org/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pharmcat", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "piranha", - "Galaxy tool ids": [ - "piranha" - ], - "Description": "Piranha is a peak-caller for CLIP- and RIP-Seq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "piranha", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/piranha", - "Galaxy wrapper version": "1.2.1.0", - "Conda id": "piranha", - "Conda version": "1.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "platypus", - "Galaxy tool ids": [ - "bg_platypus" - ], - "Description": "efficient and accurate variant-detection in high-throughput sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.well.ox.ac.uk/platypus", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "platypus", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/platypus", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/platypus", - "Galaxy wrapper version": "0.0.11", - "Conda id": "platypus", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plotly_ml_performance_plots", - "Galaxy tool ids": [ - "plotly_ml_performance_plots" - ], - "Description": "performance plots for machine learning problems", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "plotly_ml_performance_plots", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots", - "Galaxy wrapper version": "0.3", - "Conda id": "galaxy-ml", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plotly_parallel_coordinates_plot", - "Galaxy tool ids": [ - "plotly_parallel_coordinates_plot" - ], - "Description": "parallel coordinates plot produced with plotly", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://plot.ly/python/parallel-coordinates-plot/", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "plotly_parallel_coordinates_plot", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot", - "Galaxy wrapper version": "0.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plotly_regression_performance_plots", - "Galaxy tool ids": [ - "plotly_regression_performance_plots" - ], - "Description": "performance plots for regression problems", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://scikit-learn.org/stable/supervised_learning.html#supervised-learning", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "plotly_regression_performance_plots", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots", - "Galaxy wrapper version": "0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "protease_prediction", - "Galaxy tool ids": [ - "eden_protease_prediction" - ], - "Description": "This tool can learn the cleavage specificity of a given class of proteases.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/fabriziocosta/eden", - "ToolShed categories": [ - "Sequence Analysis", - "Proteomics" - ], - "ToolShed id": "protease_prediction", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction", - "Galaxy wrapper version": "0.9", - "Conda id": "eden", - "Conda version": "2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "protein_properties", - "Galaxy tool ids": [ - "bg_protein_properties" - ], - "Description": "Calculation of various properties from given protein sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "protein_properties", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties", - "Galaxy wrapper version": "0.2.0", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "improviser", - "Galaxy tool ids": [ - "proteomics_improviser" - ], - "Description": "Visualisation of PepXML files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.improviser.uni-freiburg.de/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomics_improviser", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser", - "Galaxy wrapper version": "1.1.0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "racon", - "Galaxy tool ids": [ - "racon" - ], - "Description": "Consensus module for raw de novo DNA assembly of long uncorrected reads.", - "bio.tool id": "Racon", - "bio.tool ids": [ - "Racon" - ], - "biii": null, - "bio.tool name": "Racon", - "bio.tool description": "Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.", - "EDAM operation": [ - "Genome assembly", - "Mapping assembly" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/isovic/racon", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "racon", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/racon", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/racon", - "Galaxy wrapper version": "1.5.0", - "Conda id": "racon", - "Conda version": "1.5.0", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Mapping assembly" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "repeat_masker", - "Galaxy tool ids": [ - "repeatmasker_wrapper" - ], - "Description": "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.repeatmasker.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "repeat_masker", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker", - "Galaxy wrapper version": "0.1.2", - "Conda id": "RepeatMasker", - "Conda version": "4.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "replaceColumn", - "Galaxy tool ids": [ - "replace_column_with_key_value_file" - ], - "Description": "A tool to replace all column entries of a file given by values of a key-value file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "replace_column_by_key_value_file", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn", - "Galaxy wrapper version": "0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rest_tool", - "Galaxy tool ids": [ - "pubchem_rest_tool" - ], - "Description": "This tool fetches data from pubchem via the PubChem REST API.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "pubchem_rest_tool", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool", - "Galaxy wrapper version": "0.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "antarna", - "Galaxy tool ids": [ - "antarna" - ], - "Description": "antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "antarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna", - "Galaxy wrapper version": "1.1", - "Conda id": "antarna", - "Conda version": "2.0.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "aresite2", - "Galaxy tool ids": [ - "AREsite2_REST" - ], - "Description": "AREsite2 REST Interface", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rna.tbi.univie.ac.at/AREsite", - "ToolShed categories": [ - "RNA", - "Data Source", - "Sequence Analysis" - ], - "ToolShed id": "aresite2", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2", - "Galaxy wrapper version": "0.1.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blockclust", - "Galaxy tool ids": [ - "blockclust" - ], - "Description": "BlockClust detects transcripts with similar processing patterns.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "blockclust", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust", - "Galaxy wrapper version": "1.1.1", - "Conda id": "blockclust", - "Conda version": "1.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cmsearch_deoverlap", - "Galaxy tool ids": [ - "cmsearch_deoverlap" - ], - "Description": "removes lower scoring overlaps from cmsearch results.", - "bio.tool id": "cmsearch-deoverlap", - "bio.tool ids": [ - "cmsearch-deoverlap" - ], - "biii": null, - "bio.tool name": "cmsearch-deoverlap", - "bio.tool description": "Removes lower scoring overlaps from cmsearch results.", - "EDAM operation": [ - "Comparison", - "Alignment" - ], - "EDAM topic": [ - "Biology", - "Medicine" - ], - "Status": "To update", - "Source": "https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "cmsearch_deoverlap", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap", - "Galaxy wrapper version": "0.08+galaxy2", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Comparison", - "Alignment" - ], - "EDAM topic (no superclasses)": [ - "Biology", - "Medicine" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cmv", - "Galaxy tool ids": [ - "cmcv", - "cmv", - "hmmcv", - "hmmv" - ], - "Description": "cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/eggzilla/cmv", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "cmv", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv", - "Galaxy wrapper version": "1.0.8", - "Conda id": "cmv", - "Conda version": "1.0.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cofold", - "Galaxy tool ids": [ - "cofold" - ], - "Description": "Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.e-rna.org/cofold/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "cofold", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold", - "Galaxy wrapper version": "2.0.4.0", - "Conda id": "cofold", - "Conda version": "2.0.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "compalignp", - "Galaxy tool ids": [ - "compalignp" - ], - "Description": "Compute fractional identity between trusted alignment and test alignment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "compalignp", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp", - "Galaxy wrapper version": "1.0", - "Conda id": "compalignp", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "coprarna", - "Galaxy tool ids": [ - "coprarna" - ], - "Description": "Target prediction for prokaryotic trans-acting small RNAs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/PatrickRWright/CopraRNA", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "coprarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/PatrickRWright/CopraRNA", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna", - "Galaxy wrapper version": "2.1.1", - "Conda id": "coprarna", - "Conda version": "2.1.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dewseq", - "Galaxy tool ids": [ - "dewseq" - ], - "Description": "DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "CLIP-seq" - ], - "ToolShed id": "dewseq", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq", - "Galaxy wrapper version": "0.1.0+galaxy0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dorina", - "Galaxy tool ids": [ - "dorina_search" - ], - "Description": "data source for RNA interactions in post-transcriptional regulation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA", - "Data Source" - ], - "ToolShed id": "dorina", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina", - "Galaxy wrapper version": "1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dot2ct", - "Galaxy tool ids": [ - "rnastructure_dot2ct" - ], - "Description": "Dot-Bracket to Connect Table (CT)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "dot2ct", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct", - "Galaxy wrapper version": "5.7.a", - "Conda id": "rnastructure", - "Conda version": "6.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dotknot", - "Galaxy tool ids": [ - "dotknot" - ], - "Description": "DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://dotknot.csse.uwa.edu.au/", - "ToolShed categories": [ - "RNA", - "Proteomics" - ], - "ToolShed id": "dotknot", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot", - "Galaxy wrapper version": "1.3.1", - "Conda id": "vienna_rna", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "exparna", - "Galaxy tool ids": [ - "exparna" - ], - "Description": "ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "exparna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna", - "Galaxy wrapper version": "1.0.1", - "Conda id": "exparna", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphprot", - "Galaxy tool ids": [ - "graphprot_predict_profile" - ], - "Description": "GraphProt models binding preferences of RNA-binding proteins.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/dmaticzka/GraphProt", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "CLIP-seq" - ], - "ToolShed id": "graphprot", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot", - "Galaxy wrapper version": "1.1.7+galaxy1", - "Conda id": "graphprot", - "Conda version": "1.1.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "htseq-clip", - "Galaxy tool ids": [ - "htseq_clip" - ], - "Description": "htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/EMBL-Hentze-group/htseq-clip", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "CLIP-seq" - ], - "ToolShed id": "htseq_clip", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip", - "Galaxy wrapper version": "0.1.0+galaxy0", - "Conda id": "htseq-clip", - "Conda version": "2.19.0b0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "infernal", - "Galaxy tool ids": [ - "infernal_cmalign", - "infernal_cmbuild", - "infernal_cmpress", - "infernal_cmscan", - "infernal_cmsearch", - "infernal_cmstat" - ], - "Description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities.", - "bio.tool id": "infernal", - "bio.tool ids": [ - "infernal" - ], - "biii": null, - "bio.tool name": "Infernal", - "bio.tool description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.", - "EDAM operation": [ - "Nucleic acid feature detection" - ], - "EDAM topic": [ - "Sequence sites, features and motifs", - "Structural genomics" - ], - "Status": "To update", - "Source": "http://infernal.janelia.org/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "infernal", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/infernal", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal", - "Galaxy wrapper version": "1.1.4", - "Conda id": "infernal", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [ - "Nucleic acid feature detection" - ], - "EDAM topic (no superclasses)": [ - "Sequence sites, features and motifs", - "Structural genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "inforna", - "Galaxy tool ids": [], - "Description": "INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "inforna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "intarna", - "Galaxy tool ids": [ - "intarna" - ], - "Description": "Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/BackofenLab/IntaRNA", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "intarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna", - "Galaxy wrapper version": "3.4.0", - "Conda id": "intarna", - "Conda version": "3.4.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kinwalker", - "Galaxy tool ids": [], - "Description": "Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.bioinf.uni-leipzig.de/Software/Kinwalker/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "kinwalker", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "locarna", - "Galaxy tool ids": [ - "locarna_exparnap", - "locarna_multiple", - "locarna_pairwise", - "locarna_pairwise_p", - "locarna_reliability_profile" - ], - "Description": "LocARNA - A suite for multiple alignment and folding of RNAs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.bioinf.uni-freiburg.de/Software/LocARNA/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "locarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna", - "Galaxy wrapper version": "1.9.2.3", - "Conda id": "locarna", - "Conda version": "2.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mea", - "Galaxy tool ids": [ - "mea" - ], - "Description": "Maximum expected accuracy prediction", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.bioinf.uni-leipzig.de/Software/mea", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "mea", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea", - "Galaxy wrapper version": "0.6.4.1", - "Conda id": "mea", - "Conda version": "0.6.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mqc", - "Galaxy tool ids": [ - "mqc" - ], - "Description": "Ribosome profiling mapping quality control tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Biobix/mQC", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mqc", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc", - "Galaxy wrapper version": "1.9", - "Conda id": "mqc", - "Conda version": "1.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nastiseq", - "Galaxy tool ids": [ - "nastiseq" - ], - "Description": "A method to identify cis-NATs using ssRNA-seq", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "nastiseq", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq", - "Galaxy wrapper version": "1.0", - "Conda id": "r-nastiseq", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "paralyzer", - "Galaxy tool ids": [ - "paralyzer" - ], - "Description": "A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "paralyzer", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer", - "Galaxy wrapper version": "1.5", - "Conda id": "paralyzer", - "Conda version": "1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pipmir", - "Galaxy tool ids": [ - "pipmir" - ], - "Description": "A method to identify novel plant miRNA.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "pipmir", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir", - "Galaxy wrapper version": "0.1.0", - "Conda id": "pipmir", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rRNA", - "Galaxy tool ids": [ - "meta_rna" - ], - "Description": "Identification of ribosomal RNA genes in metagenomic fragments.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://weizhong-lab.ucsd.edu/meta_rna/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rrna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rRNA", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA", - "Galaxy wrapper version": "0.1", - "Conda id": "hmmsearch3.0", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rbpbench", - "Galaxy tool ids": [ - "rbpbench" - ], - "Description": "Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs", - "bio.tool id": "rbpbench", - "bio.tool ids": [ - "rbpbench" - ], - "biii": null, - "bio.tool name": "RBPBench", - "bio.tool description": "Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs", - "EDAM operation": [], - "EDAM topic": [ - "RNA", - "Protein interactions", - "RNA immunoprecipitation", - "Bioinformatics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/michauhl/RBPBench", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "CLIP-seq" - ], - "ToolShed id": "rbpbench", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench", - "Galaxy wrapper version": "0.8.1", - "Conda id": "rbpbench", - "Conda version": "0.8.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "RNA", - "Protein interactions", - "RNA immunoprecipitation", - "Bioinformatics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rcas", - "Galaxy tool ids": [ - "rcas" - ], - "Description": "RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/BIMSBbioinfo/RCAS", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rcas", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas", - "Galaxy wrapper version": "1.5.4", - "Conda id": "bioconductor-rcas", - "Conda version": "1.28.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "reago", - "Galaxy tool ids": [ - "reago" - ], - "Description": "Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.", - "bio.tool id": "reago", - "bio.tool ids": [ - "reago" - ], - "biii": null, - "bio.tool name": "REAGO", - "bio.tool description": "This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.", - "EDAM operation": [ - "Sequence assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "RNA", - "Metagenomics", - "Microbiology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/chengyuan/reago-1.1", - "ToolShed categories": [ - "Metagenomics", - "RNA" - ], - "ToolShed id": "reago", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago", - "Galaxy wrapper version": "1.1", - "Conda id": "reago", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [ - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "RNA", - "Metagenomics", - "Microbiology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "remurna", - "Galaxy tool ids": [ - "remurna" - ], - "Description": "remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "remurna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna", - "Galaxy wrapper version": "1.0.0", - "Conda id": "remurna", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ribotaper", - "Galaxy tool ids": [ - "ribotaper_create_annotation", - "ribotaper_create_metaplots", - "ribotaper_ribosome_profiling" - ], - "Description": "A method for defining traslated ORFs using Ribosome Profiling data.", - "bio.tool id": "ribotaper", - "bio.tool ids": [ - "ribotaper" - ], - "biii": null, - "bio.tool name": "RiboTaper", - "bio.tool description": "New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.", - "EDAM operation": [ - "Gene expression profiling" - ], - "EDAM topic": [ - "Functional genomics" - ], - "Status": "To update", - "Source": "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "ribotaper", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper", - "Galaxy wrapper version": "1.3.1a", - "Conda id": "ribotaper", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [ - "Gene expression profiling" - ], - "EDAM topic (no superclasses)": [ - "Functional genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rna_shapes", - "Galaxy tool ids": [ - "RNAshapes" - ], - "Description": "Compute secondary structures of RNA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnashapes", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes", - "Galaxy wrapper version": "3.3.0", - "Conda id": "@EXECUTABLE@", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnabob", - "Galaxy tool ids": [ - "rbc_rnabob" - ], - "Description": "Fast pattern searching for RNA structural motifs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://eddylab.org/software.html", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnabob", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob", - "Galaxy wrapper version": "2.2.1.0", - "Conda id": "rnabob", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnacode", - "Galaxy tool ids": [ - "rbc_rnacode" - ], - "Description": "Analyze the protein coding potential in MSA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnacode", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode", - "Galaxy wrapper version": "0.3.2", - "Conda id": "rnacode", - "Conda version": "0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnacommender", - "Galaxy tool ids": [ - "rbc_rnacommender" - ], - "Description": "RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/gianlucacorrado/RNAcommender", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnacommender", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender", - "Galaxy wrapper version": "0.1.1", - "Conda id": "sam", - "Conda version": "3.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnalien", - "Galaxy tool ids": [ - "RNAlien" - ], - "Description": "RNAlien unsupervized RNA family model construction", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rna.tbi.univie.ac.at/rnalien/", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "rnalien", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien", - "Galaxy wrapper version": "1.3.6", - "Conda id": "rnalien", - "Conda version": "1.8.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnasnp", - "Galaxy tool ids": [ - "rnasnp" - ], - "Description": "RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rth.dk/resources/rnasnp/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnasnp", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp", - "Galaxy wrapper version": "1.2.0", - "Conda id": "rnasnp", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnaz", - "Galaxy tool ids": [ - "rnaz", - "rnaz_annotate", - "rnaz_cluster", - "rnaz_randomize_aln", - "rnaz_select_seqs", - "rnaz_window" - ], - "Description": "RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://www.tbi.univie.ac.at/~wash/RNAz/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "rnaz", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz", - "Galaxy wrapper version": "2.1.1", - "Conda id": "rnaz", - "Conda version": "2.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "selectsequencesfrommsa", - "Galaxy tool ids": [ - "selectsequencesfrommsa" - ], - "Description": "SelectSequences - selects representative entries from a multiple sequence alignment in clustal format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/eggzilla/SelectSequences", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "selectsequencesfrommsa", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa", - "Galaxy wrapper version": "1.0.5", - "Conda id": "selectsequencesfrommsa", - "Conda version": "1.0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sortmerna", - "Galaxy tool ids": [ - "bg_sortmerna" - ], - "Description": "SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.", - "bio.tool id": "sortmerna", - "bio.tool ids": [ - "sortmerna" - ], - "biii": null, - "bio.tool name": "SortMeRNA", - "bio.tool description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.", - "EDAM operation": [ - "Sequence similarity search", - "Sequence comparison", - "Sequence alignment analysis" - ], - "EDAM topic": [ - "Metatranscriptomics", - "Metagenomics" - ], - "Status": "To update", - "Source": "http://bioinfo.lifl.fr/RNA/sortmerna/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "sortmerna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna", - "Galaxy wrapper version": "4.3.6", - "Conda id": "sortmerna", - "Conda version": "4.3.7", - "EDAM operation (no superclasses)": [ - "Sequence similarity search", - "Sequence alignment analysis" - ], - "EDAM topic (no superclasses)": [ - "Metatranscriptomics", - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "sshmm", - "Galaxy tool ids": [ - "sshmm" - ], - "Description": "ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.molgen.mpg.de/heller/ssHMM", - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "sshmm", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm", - "Galaxy wrapper version": "1.0.7", - "Conda id": "sshmm", - "Conda version": "1.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "targetfinder", - "Galaxy tool ids": [ - "targetfinder" - ], - "Description": "Plant small RNA target prediction tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/carringtonlab/TargetFinder.git", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "targetfinder", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder", - "Galaxy wrapper version": "1.7", - "Conda id": "targetfinder", - "Conda version": "1.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "trna_prediction", - "Galaxy tool ids": [ - "aragorn_trna", - "trnascan" - ], - "Description": "Aragorn predicts tRNA and tmRNA in nucleotide sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://mbioserv2.mbioekol.lu.se/ARAGORN/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "trna_prediction", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction", - "Galaxy wrapper version": "0.6", - "Conda id": "aragorn", - "Conda version": "1.2.41", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vienna_rna", - "Galaxy tool ids": [ - "viennarna_kinfold", - "viennarna_kinwalker", - "viennarna_rna2dfold", - "viennarna_rnaaliduplex", - "viennarna_rnaalifold", - "viennarna_rnacofold", - "viennarna_rnadistance", - "viennarna_rnaduplex", - "viennarna_rnaeval", - "viennarna_rnafold", - "viennarna_rnaheat", - "viennarna_rnainverse", - "viennarna_rnalalifold", - "viennarna_rnalfold", - "viennarna_rnapaln", - "viennarna_rnadpdist", - "viennarna_rnapkplex", - "viennarna_rnaplex", - "viennarna_rnaplfold", - "viennarna_rnaplot", - "viennarna_rnasnoop", - "viennarna_rnasubopt", - "viennarna_rnaup" - ], - "Description": "ViennaRNA - Prediction and comparison of RNA secondary structures", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.tbi.univie.ac.at/RNA/", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "viennarna", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna", - "Galaxy wrapper version": "2.2.10", - "Conda id": "viennarna", - "Conda version": "2.6.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 21, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sailfish", - "Galaxy tool ids": [ - "sailfish" - ], - "Description": "Sailfish is a tool for transcript quantification from RNA-seq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.cs.cmu.edu/~ckingsf/software/sailfish/", - "ToolShed categories": [ - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "sailfish", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sailfish", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sailfish", - "Galaxy wrapper version": "0.10.1.1", - "Conda id": "bzip2", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "salmon", - "Galaxy tool ids": [ - "alevin", - "salmon", - "salmonquantmerge" - ], - "Description": "Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.", - "bio.tool id": "salmon", - "bio.tool ids": [ - "salmon" - ], - "biii": null, - "bio.tool name": "Salmon", - "bio.tool description": "A tool for transcript expression quantification from RNA-seq data", - "EDAM operation": [ - "Sequence composition calculation", - "RNA-Seq quantification", - "Gene expression analysis" - ], - "EDAM topic": [ - "RNA-Seq", - "Gene expression", - "Transcriptomics" - ], - "Status": "To update", - "Source": "https://github.com/COMBINE-lab/salmon", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/salmon", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/salmon", - "Galaxy wrapper version": "1.10.1", - "Conda id": "salmon", - "Conda version": "1.10.3", - "EDAM operation (no superclasses)": [ - "Sequence composition calculation", - "RNA-Seq quantification", - "Gene expression analysis" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Transcriptomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "sambamba", - "Galaxy tool ids": [ - "sambamba_flagstat", - "sambamba_markdup", - "sambamba_merge", - "sambamba_slice", - "sambamba_sort", - "sambamba_view", - "sambamba_depth" - ], - "Description": "SAMBAMBA: process your BAM data faster!", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/lomereiter/sambamba", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "sambamba", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sambamba", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sambamba", - "Galaxy wrapper version": null, - "Conda id": "sambamba", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sed", - "Galaxy tool ids": [ - "sed_stream_editor" - ], - "Description": "Manipulate your data with the sed command line tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "sed_wrapper", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", - "Galaxy wrapper version": "0.0.1", - "Conda id": "sed", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "segemehl", - "Galaxy tool ids": [ - "segemehl" - ], - "Description": "segemehl - short read mapping with gaps", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.bioinf.uni-leipzig.de/Software/segemehl/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "segemehl", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/segemehl", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/segemehl", - "Galaxy wrapper version": "0.2.0.4", - "Conda id": "segemehl", - "Conda version": "0.3.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sklearn", - "Galaxy tool ids": [ - "sklearn_mlxtend_association_rules", - "sklearn_clf_metrics", - "sklearn_discriminant_classifier", - "sklearn_ensemble", - "sklearn_estimator_attributes", - "sklearn_feature_selection", - "sklearn_fitted_model_eval", - "sklearn_generalized_linear", - "keras_batch_models", - "keras_model_builder", - "keras_model_config", - "keras_train_and_eval", - "sklearn_label_encoder", - "sklearn_lightgbm", - "ml_visualization_ex", - "model_prediction", - "sklearn_model_validation", - "sklearn_nn_classifier", - "sklearn_numeric_clustering", - "sklearn_pairwise_metrics", - "sklearn_pca", - "sklearn_build_pipeline", - "sklearn_data_preprocess", - "sklearn_regression_metrics", - "sklearn_sample_generator", - "sklearn_searchcv", - "sklearn_model_fit", - "scipy_sparse", - "stacking_ensemble_models", - "sklearn_svm_classifier", - "sklearn_to_categorical", - "sklearn_train_test_eval", - "sklearn_train_test_split" - ], - "Description": "Machine Learning tool suite from Scikit-learn", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://scikit-learn.org", - "ToolShed categories": [ - "Machine Learning", - "Statistics" - ], - "ToolShed id": "sklearn", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sklearn", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sklearn", - "Galaxy wrapper version": "1.0.11.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 30, - "Available on UseGalaxy.org.au": 14, - "Available on UseGalaxy.eu": 31, - "Available on UseGalaxy.org.fr": 16 - }, - { - "Galaxy wrapper id": "splitfasta", - "Galaxy tool ids": [ - "rbc_splitfasta" - ], - "Description": "Split a multi-sequence fasta file into files containing single sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "splitfasta", - "Galaxy wrapper owner": "rnateam", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta", - "Galaxy wrapper version": "0.4.0", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "statistics", - "Galaxy tool ids": [ - "bg_statistical_hypothesis_testing" - ], - "Description": "Tool for computing statistical tests.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "bg_statistical_hypothesis_testing", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", - "Galaxy wrapper version": "0.3", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "stress_ng", - "Galaxy tool ids": [ - "stress_ng" - ], - "Description": "stress test a computer system in various selectable ways", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Web Services" - ], - "ToolShed id": "stress_ng", - "Galaxy wrapper owner": "bgruening-util", - "Galaxy wrapper source": "https://github.com/ColinIanKing/stress-ng", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng", - "Galaxy wrapper version": "0.12.04", - "Conda id": "stress-ng", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tapscan", - "Galaxy tool ids": [ - "tapscan_classify" - ], - "Description": "Search for transcription associated proteins (TAPs)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://plantcode.cup.uni-freiburg.de/tapscan/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "tapscan", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tapscan", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tapscan", - "Galaxy wrapper version": "4.76+galaxy0", - "Conda id": "hmmer", - "Conda version": "3.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "add_line_to_file", - "Galaxy tool ids": [ - "add_line_to_file" - ], - "Description": "Adds a text line to the beginning or end of a file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "add_line_to_file", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file", - "Galaxy wrapper version": "0.1.0", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "column_arrange_by_header", - "Galaxy tool ids": [ - "bg_column_arrange_by_header" - ], - "Description": "Column arrange by header name", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "column_arrange_by_header", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header", - "Galaxy wrapper version": "0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "join_files_on_column_fuzzy", - "Galaxy tool ids": [ - "join_files_on_column_fuzzy" - ], - "Description": "Join two files on a common column, allowing a certain difference.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "join_files_on_column_fuzzy", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "split_file_on_column", - "Galaxy tool ids": [ - "tp_split_on_column" - ], - "Description": "Split a file on a specific column.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "split_file_on_column", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column", - "Galaxy wrapper version": "0.6", - "Conda id": "gawk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "split_file_to_collection", - "Galaxy tool ids": [ - "split_file_to_collection" - ], - "Description": "Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "split_file_to_collection", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", - "Galaxy wrapper version": "0.5.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "text_processing", - "Galaxy tool ids": [ - "tp_awk_tool", - "tp_cat", - "tp_cut_tool", - "tp_easyjoin_tool", - "tp_find_and_replace", - "tp_grep_tool", - "tp_head_tool", - "tp_multijoin_tool", - "nl", - "tp_text_file_with_recurring_lines", - "tp_replace_in_column", - "tp_replace_in_line", - "tp_sed_tool", - "tp_sort_header_tool", - "tp_sort_rows", - "tp_uniq_tool", - "tp_tac", - "tp_tail_tool", - "tp_unfold_column_tool", - "tp_sorted_uniq" - ], - "Description": "High performance text processing tools using the GNU coreutils, sed, awk and friends.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.gnu.org/software/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "text_processing", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing", - "Galaxy wrapper version": "9.3", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 20, - "Available on UseGalaxy.org.au": 20, - "Available on UseGalaxy.eu": 20, - "Available on UseGalaxy.org.fr": 20 - }, - { - "Galaxy wrapper id": "tgsgapcloser", - "Galaxy tool ids": [ - "tgsgapcloser" - ], - "Description": "TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.", - "bio.tool id": "TGS-GapCloser", - "bio.tool ids": [ - "TGS-GapCloser" - ], - "biii": null, - "bio.tool name": "TGS-GapCloser", - "bio.tool description": "TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.", - "EDAM operation": [ - "Genome assembly", - "Read mapping", - "Scaffolding", - "Localised reassembly" - ], - "EDAM topic": [ - "Sequencing", - "Sequence assembly", - "Phylogeny", - "Transcription factors and regulatory sites", - "Mapping" - ], - "Status": "To update", - "Source": "https://github.com/BGI-Qingdao/TGS-GapCloser", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "tgsgapcloser", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser", - "Galaxy wrapper version": "1.0.3", - "Conda id": "tgsgapcloser", - "Conda version": "1.2.1", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Read mapping", - "Scaffolding", - "Localised reassembly" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence assembly", - "Phylogeny", - "Transcription factors and regulatory sites", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tiara", - "Galaxy tool ids": [ - "tiara" - ], - "Description": "Tool for identification of eukaryotic sequences in the metagenomic datasets.", - "bio.tool id": "Tiara", - "bio.tool ids": [ - "Tiara" - ], - "biii": null, - "bio.tool name": "TIARA", - "bio.tool description": "Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).", - "EDAM operation": [ - "Genome comparison", - "Data retrieval", - "Variant calling", - "Genome visualisation", - "Structural variation detection" - ], - "EDAM topic": [ - "Sequencing", - "Genomics", - "DNA polymorphism", - "DNA structural variation" - ], - "Status": "To update", - "Source": "https://github.com/ibe-uw/tiara", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": "tiara", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tiara", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tiara", - "Galaxy wrapper version": "1.0.3", - "Conda id": "tiara", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Genome comparison", - "Data retrieval", - "Variant calling", - "Genome visualisation", - "Structural variation detection" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Genomics", - "DNA polymorphism" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tool_recommendation_model", - "Galaxy tool ids": [ - "create_tool_recommendation_model" - ], - "Description": "Create model to recommend tools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "create_tool_recommendation_model", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model", - "Galaxy wrapper version": "0.0.5", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "trim_galore", - "Galaxy tool ids": [ - "trim_galore" - ], - "Description": "Trim Galore adaptive quality and adapter trimmer", - "bio.tool id": "trim_galore", - "bio.tool ids": [ - "trim_galore" - ], - "biii": null, - "bio.tool name": "Trim Galore", - "bio.tool description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.", - "EDAM operation": [ - "Sequence trimming", - "Primer removal", - "Read pre-processing" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", - "ToolShed categories": [ - "Sequence Analysis", - "Fastq Manipulation" - ], - "ToolShed id": "trim_galore", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore", - "Galaxy wrapper version": "0.6.7", - "Conda id": "trim-galore", - "Conda version": "0.6.10", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "Primer removal", - "Read pre-processing" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "uniprot_rest_interface", - "Galaxy tool ids": [ - "uniprot" - ], - "Description": "UniProt ID mapping and sequence retrieval", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/jdrudolph/uniprot", - "ToolShed categories": [ - "Proteomics", - "Sequence Analysis" - ], - "ToolShed id": "uniprot_rest_interface", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface", - "Galaxy wrapper version": "0.5", - "Conda id": "requests", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vt", - "Galaxy tool ids": [ - "vt_@BINARY@", - "vt_@BINARY@" - ], - "Description": "A tool set for short variant discovery in genetic sequence data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "vt", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/atks/vt", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/vt", - "Galaxy wrapper version": "0.2", - "Conda id": "vt", - "Conda version": "2015.11.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "whisper", - "Galaxy tool ids": [ - "whisper" - ], - "Description": "Transcribe audio or video files to text using the OpenAI Whisper.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "whisper", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", - "Galaxy wrapper version": "20231117", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "wtdbg", - "Galaxy tool ids": [ - "wtdbg" - ], - "Description": "WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.", - "bio.tool id": "wtdbg2", - "bio.tool ids": [ - "wtdbg2" - ], - "biii": null, - "bio.tool name": "wtdbg2", - "bio.tool description": "Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.", - "EDAM operation": [ - "Genome assembly", - "De-novo assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/ruanjue/wtdbg2", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "wtdbg", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg", - "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg", - "Galaxy wrapper version": "2.5", - "Conda id": "wtdbg", - "Conda version": "2.5", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "align_back_trans", - "Galaxy tool ids": [ - "align_back_trans" - ], - "Description": "Thread nucleotides onto a protein alignment (back-translation)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "align_back_trans", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", - "Galaxy wrapper version": "0.0.10", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chromosome_diagram", - "Galaxy tool ids": [ - "chromosome_diagram" - ], - "Description": "Chromosome Diagrams using Biopython", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics", - "Sequence Analysis", - "Visualization" - ], - "ToolShed id": "chromosome_diagram", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram", - "Galaxy wrapper version": "0.0.3", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "clc_assembly_cell", - "Galaxy tool ids": [ - "clc_assembler", - "clc_mapper" - ], - "Description": "Galaxy wrapper for the CLC Assembly Cell suite from CLCBio", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", - "ToolShed categories": [ - "Assembly", - "Next Gen Mappers", - "SAM" - ], - "ToolShed id": "clc_assembly_cell", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", - "Galaxy wrapper version": "0.0.7", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "clinod", - "Galaxy tool ids": [ - "clinod" - ], - "Description": "NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins", - "bio.tool id": "clinod", - "bio.tool ids": [ - "clinod" - ], - "biii": null, - "bio.tool name": "clinod", - "bio.tool description": "The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.", - "EDAM operation": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.compbio.dundee.ac.uk/www-nod/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "clinod", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod", - "Galaxy wrapper version": "0.1.0", - "Conda id": "clinod", - "Conda version": "1.3", - "EDAM operation (no superclasses)": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "count_roi_variants", - "Galaxy tool ids": [ - "count_roi_variants" - ], - "Description": "Count sequence variants in region of interest in BAM file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", - "ToolShed categories": [ - "Assembly", - "SAM" - ], - "ToolShed id": "count_roi_variants", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", - "Galaxy wrapper version": "0.0.6", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "coverage_stats", - "Galaxy tool ids": [ - "coverage_stats" - ], - "Description": "BAM coverage statistics using samtools idxstats and depth", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", - "ToolShed categories": [ - "Assembly", - "SAM" - ], - "ToolShed id": "coverage_stats", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", - "Galaxy wrapper version": "0.1.0", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "effectiveT3", - "Galaxy tool ids": [ - "effectiveT3" - ], - "Description": "Find bacterial type III effectors in protein sequences", - "bio.tool id": "effectivet3", - "bio.tool ids": [ - "effectivet3" - ], - "biii": null, - "bio.tool name": "EffectiveT3", - "bio.tool description": "Prediction of putative Type-III secreted proteins.", - "EDAM operation": [ - "Sequence classification" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://effectors.org", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "effectivet3", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3", - "Galaxy wrapper version": "0.0.21", - "Conda id": "effectiveT3", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [ - "Sequence classification" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_filter_by_id", - "Galaxy tool ids": [ - "fasta_filter_by_id" - ], - "Description": "Filter FASTA sequences by ID (DEPRECATED)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "fasta_filter_by_id", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", - "Galaxy wrapper version": "0.0.7", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_filter_by_id", - "Galaxy tool ids": [ - "fastq_filter_by_id" - ], - "Description": "Filter FASTQ sequences by ID (DEPRECATED)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", - "ToolShed categories": [ - "Fastq Manipulation", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "fastq_filter_by_id", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", - "Galaxy wrapper version": "0.0.7", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_pair_names", - "Galaxy tool ids": [ - "fastq_pair_names" - ], - "Description": "Extract FASTQ paired read names", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fastq_pair_names", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", - "Galaxy wrapper version": "0.0.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_paired_unpaired", - "Galaxy tool ids": [ - "fastq_paired_unpaired" - ], - "Description": "Divide FASTQ file into paired and unpaired reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", - "ToolShed categories": [ - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "fastq_paired_unpaired", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", - "Galaxy wrapper version": "0.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "get_orfs_or_cdss", - "Galaxy tool ids": [ - "get_orfs_or_cdss" - ], - "Description": "Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "get_orfs_or_cdss", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", - "Galaxy wrapper version": "0.2.3", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "mummer", - "Galaxy tool ids": [ - "mummerplot_wrapper" - ], - "Description": "Draw dotplots using mummer, mucmer, or promer with mummerplot", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://mummer.sourceforge.net/", - "ToolShed categories": [ - "Graphics", - "Sequence Analysis", - "Visualization" - ], - "ToolShed id": "mummer", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer", - "Galaxy wrapper version": "0.0.8", - "Conda id": "ghostscript", - "Conda version": "9.18", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nlstradamus", - "Galaxy tool ids": [ - "nlstradamus" - ], - "Description": "Find nuclear localization signals (NLSs) in protein sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.moseslab.csb.utoronto.ca/NLStradamus", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "nlstradamus", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus", - "Galaxy wrapper version": "0.0.11", - "Conda id": "NLStradamus", - "Conda version": "1.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "predictnls", - "Galaxy tool ids": [ - "predictnls" - ], - "Description": "Python reimplementation of predictNLS for Galaxy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "predictnls", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", - "Galaxy wrapper version": "0.0.10", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "protein_analysis", - "Galaxy tool ids": [ - "promoter2", - "Psortb", - "rxlr_motifs", - "signalp3", - "tmhmm2", - "wolf_psort" - ], - "Description": "TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tmhmm_and_signalp", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", - "Galaxy wrapper version": "0.0.13", - "Conda id": "promoter", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sample_seqs", - "Galaxy tool ids": [ - "sample_seqs" - ], - "Description": "Sub-sample sequences files (e.g. to reduce coverage)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", - "ToolShed categories": [ - "Assembly", - "Fasta Manipulation", - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "sample_seqs", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", - "Galaxy wrapper version": "0.2.6", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "samtools_depad", - "Galaxy tool ids": [ - "samtools_depad" - ], - "Description": "Re-align a SAM/BAM file with a padded reference (using samtools depad)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.htslib.org/", - "ToolShed categories": [ - "Assembly", - "SAM", - "Sequence Analysis" - ], - "ToolShed id": "samtools_depad", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad", - "Galaxy wrapper version": "0.0.5", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "samtools_depth", - "Galaxy tool ids": [ - "samtools_depth" - ], - "Description": "Coverage depth via samtools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.htslib.org/", - "ToolShed categories": [ - "Assembly", - "Sequence Analysis", - "SAM" - ], - "ToolShed id": "samtools_depth", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth", - "Galaxy wrapper version": "0.0.3", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "samtools_idxstats", - "Galaxy tool ids": [ - "samtools_idxstats" - ], - "Description": "BAM mapping statistics (using samtools idxstats)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.htslib.org/", - "ToolShed categories": [ - "Assembly", - "Next Gen Mappers", - "SAM" - ], - "ToolShed id": "samtools_idxstats", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats", - "Galaxy wrapper version": "0.0.6", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "seq_composition", - "Galaxy tool ids": [ - "seq_composition" - ], - "Description": "Sequence composition", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seq_composition", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", - "Galaxy wrapper version": "0.0.5", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "seq_filter_by_id", - "Galaxy tool ids": [ - "seq_filter_by_id" - ], - "Description": "Filter sequences by ID", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "seq_filter_by_id", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", - "Galaxy wrapper version": "0.2.9", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "seq_filter_by_mapping", - "Galaxy tool ids": [ - "seq_filter_by_mapping" - ], - "Description": "Filter sequencing reads using SAM/BAM mapping files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", - "ToolShed categories": [ - "Assembly", - "Fasta Manipulation", - "Fastq Manipulation", - "SAM", - "Sequence Analysis" - ], - "ToolShed id": "seq_filter_by_mapping", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", - "Galaxy wrapper version": "0.0.8", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seq_length", - "Galaxy tool ids": [ - "seq_length" - ], - "Description": "Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "seq_length", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", - "Galaxy wrapper version": "0.0.5", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seq_primer_clip", - "Galaxy tool ids": [ - "seq_primer_clip" - ], - "Description": "Trim off 5' or 3' primers", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", - "ToolShed categories": [ - "Assembly", - "Fasta Manipulation", - "Text Manipulation" - ], - "ToolShed id": "seq_primer_clip", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", - "Galaxy wrapper version": "0.0.18", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seq_rename", - "Galaxy tool ids": [ - "seq_rename" - ], - "Description": "Rename sequences with ID mapping from a tabular file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "seq_rename", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", - "Galaxy wrapper version": "0.0.10", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seq_select_by_id", - "Galaxy tool ids": [ - "seq_select_by_id" - ], - "Description": "Select sequences by ID", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "seq_select_by_id", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", - "Galaxy wrapper version": "0.0.15", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "venn_list", - "Galaxy tool ids": [ - "venn_list" - ], - "Description": "Draw Venn Diagram (PDF) from lists, FASTA files, etc", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", - "ToolShed categories": [ - "Graphics", - "Sequence Analysis", - "Visualization" - ], - "ToolShed id": "venn_list", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", - "Galaxy wrapper version": "0.1.2", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - } - ], - [ - { - "Galaxy wrapper id": "TrimNs", - "Galaxy tool ids": [ - "trimns" - ], - "Description": "TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "trimns", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs", - "Galaxy wrapper version": "0.1.0", - "Conda id": "trimns_vgp", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "abricate", - "Galaxy tool ids": [ - "abricate", - "abricate_list", - "abricate_summary" - ], - "Description": "Mass screening of contigs for antiobiotic resistance genes", - "bio.tool id": "ABRicate", - "bio.tool ids": [ - "ABRicate" - ], - "biii": null, - "bio.tool name": "ABRicate", - "bio.tool description": "Mass screening of contigs for antimicrobial resistance or virulence genes.", - "EDAM operation": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic": [ - "Genomics", - "Microbiology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/tseemann/abricate", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "abricate", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate", - "Galaxy wrapper version": "1.0.1", - "Conda id": "abricate", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Microbiology" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "abritamr", - "Galaxy tool ids": [ - "abritamr" - ], - "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", - "bio.tool id": "abritamr", - "bio.tool ids": [ - "abritamr" - ], - "biii": null, - "bio.tool name": "abriTAMR", - "bio.tool description": "an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.", - "EDAM operation": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic": [ - "Microbiology", - "Public health and epidemiology", - "Infectious disease" - ], - "Status": "To update", - "Source": "https://zenodo.org/record/7370628", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "abritamr", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", - "Galaxy wrapper version": "1.0.14", - "Conda id": "abritamr", - "Conda version": "1.0.17", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Public health and epidemiology", - "Infectious disease" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "abyss", - "Galaxy tool ids": [ - "abyss-pe" - ], - "Description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", - "bio.tool id": "abyss", - "bio.tool ids": [ - "abyss" - ], - "biii": null, - "bio.tool name": "ABySS", - "bio.tool description": "De novo genome sequence assembler using short reads.", - "EDAM operation": [ - "Genome assembly", - "De-novo assembly", - "Scaffolding" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "http://www.bcgsc.ca/platform/bioinfo/software/abyss", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "abyss", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", - "Galaxy wrapper version": "2.3.7", - "Conda id": "abyss", - "Conda version": "2.3.7", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "De-novo assembly", - "Scaffolding" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "adapter_removal", - "Galaxy tool ids": [ - "adapter_removal" - ], - "Description": "Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.", - "bio.tool id": "adapterremoval", - "bio.tool ids": [ - "adapterremoval" - ], - "biii": null, - "bio.tool name": "AdapterRemoval", - "bio.tool description": "AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.", - "EDAM operation": [ - "Sequence trimming", - "Sequence merging", - "Primer removal" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/MikkelSchubert/adapterremoval", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "adapter_removal", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal", - "Galaxy wrapper version": "2.3.3", - "Conda id": "adapterremoval", - "Conda version": "2.3.3", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "Sequence merging", - "Primer removal" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "add_input_name_as_column", - "Galaxy tool ids": [ - "addName" - ], - "Description": "Add input name as column on an existing tabular file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "add_input_name_as_column", - "Galaxy wrapper owner": "mvdbeek", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column", - "Galaxy wrapper version": "0.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "aegean", - "Galaxy tool ids": [ - "aegean_canongff3", - "aegean_gaeval", - "aegean_locuspocus", - "aegean_parseval" - ], - "Description": "AEGeAn toolkit wrappers", - "bio.tool id": "gaeval", - "bio.tool ids": [ - "gaeval" - ], - "biii": null, - "bio.tool name": "GAEVAL", - "bio.tool description": "Gene Annotation EVAluation.", - "EDAM operation": [ - "Sequence annotation" - ], - "EDAM topic": [ - "Sequence analysis", - "Gene structure" - ], - "Status": "Up-to-date", - "Source": "https://github.com/BrendelGroup/AEGeAn", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "aegean", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean", - "Galaxy wrapper version": "0.16.0", - "Conda id": "aegean", - "Conda version": "0.16.0", - "EDAM operation (no superclasses)": [ - "Sequence annotation" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Gene structure" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "aldex2", - "Galaxy tool ids": [ - "aldex2" - ], - "Description": "Performs analysis Of differential abundance taking sample variation into account", - "bio.tool id": "aldex2", - "bio.tool ids": [ - "aldex2" - ], - "biii": null, - "bio.tool name": "ALDEx2", - "bio.tool description": "A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.", - "EDAM operation": [ - "Statistical inference" - ], - "EDAM topic": [ - "Gene expression", - "Statistics and probability" - ], - "Status": "To update", - "Source": "https://github.com/ggloor/ALDEx_bioc", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "aldex2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", - "Galaxy wrapper version": "1.26.0", - "Conda id": "bioconductor-aldex2", - "Conda version": "1.34.0", - "EDAM operation (no superclasses)": [ - "Statistical inference" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "allegro", - "Galaxy tool ids": [ - "allegro" - ], - "Description": "Linkage and haplotype analysis from deCODE", - "bio.tool id": "allegro", - "bio.tool ids": [ - "allegro" - ], - "biii": null, - "bio.tool name": "Allegro", - "bio.tool description": "It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.", - "EDAM operation": [ - "Sequence motif discovery" - ], - "EDAM topic": [ - "Sequence analysis", - "Transcription factors and regulatory sites", - "DNA" - ], - "Status": "To update", - "Source": "http://www.decode.com/software/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "allegro", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro", - "Galaxy wrapper version": "@VER@.0", - "Conda id": "allegro", - "Conda version": "3", - "EDAM operation (no superclasses)": [ - "Sequence motif discovery" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Transcription factors and regulatory sites", - "DNA" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "amplican", - "Galaxy tool ids": [ - "amplican" - ], - "Description": "AmpliCan is an analysis tool for genome editing.", - "bio.tool id": "amplican", - "bio.tool ids": [ - "amplican" - ], - "biii": null, - "bio.tool name": "amplican", - "bio.tool description": "It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.", - "EDAM operation": [ - "Alignment", - "Standardisation and normalisation" - ], - "EDAM topic": [ - "PCR experiment", - "Statistics and probability" - ], - "Status": "To update", - "Source": "https://github.com/valenlab/amplican", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "amplican", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican", - "Galaxy wrapper version": "1.14.0", - "Conda id": "bioconductor-amplican", - "Conda version": "1.24.0", - "EDAM operation (no superclasses)": [ - "Alignment", - "Standardisation and normalisation" - ], - "EDAM topic (no superclasses)": [ - "PCR experiment", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ampvis2", - "Galaxy tool ids": [ - "ampvis2_alpha_diversity", - "ampvis2_boxplot", - "ampvis2_core", - "ampvis2_export_fasta", - "ampvis2_frequency", - "ampvis2_heatmap", - "ampvis2_load", - "ampvis2_merge_ampvis2", - "ampvis2_mergereplicates", - "ampvis2_octave", - "ampvis2_ordinate", - "ampvis2_otu_network", - "ampvis2_rankabundance", - "ampvis2_rarecurve", - "ampvis2_setmetadata", - "ampvis2_subset_samples", - "ampvis2_subset_taxa", - "ampvis2_timeseries", - "ampvis2_venn" - ], - "Description": "ampvis2", - "bio.tool id": "ampvis", - "bio.tool ids": [ - "ampvis" - ], - "biii": null, - "bio.tool name": "ampvis", - "bio.tool description": "ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.", - "EDAM operation": [ - "Analysis", - "Visualisation" - ], - "EDAM topic": [ - "Biodiversity" - ], - "Status": "To update", - "Source": "https://github.com/MadsAlbertsen/ampvis2/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "ampvis2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2", - "Galaxy wrapper version": "2.8.6", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Analysis", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Biodiversity" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 19, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "amrfinderplus", - "Galaxy tool ids": [ - "amrfinderplus" - ], - "Description": "\"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search \"plus\", stress, heat, and biocide resistance and virulence factors for some organisms.", - "bio.tool id": "amrfinderplus", - "bio.tool ids": [ - "amrfinderplus" - ], - "biii": null, - "bio.tool name": "AMRFinderPlus", - "bio.tool description": "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search \"plus\", stress, heat, and biocide resistance and virulence factors for some organisms", - "EDAM operation": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic": [ - "Microbiology", - "Public health and epidemiology", - "Infectious disease" - ], - "Status": "Up-to-date", - "Source": "https://github.com/ncbi/amr", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "AMRFinderPlus", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus", - "Galaxy wrapper version": "3.12.8", - "Conda id": "ncbi-amrfinderplus", - "Conda version": "3.12.8", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Public health and epidemiology", - "Infectious disease" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ancombc", - "Galaxy tool ids": [ - "ancombc" - ], - "Description": "Performs analysis of compositions of microbiomes with bias correction.", - "bio.tool id": "ancombc", - "bio.tool ids": [ - "ancombc" - ], - "biii": null, - "bio.tool name": "ANCOMBC", - "bio.tool description": "Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.", - "EDAM operation": [ - "DNA barcoding" - ], - "EDAM topic": [ - "Microbial ecology", - "Metagenomics", - "Taxonomy" - ], - "Status": "To update", - "Source": "https://github.com/FrederickHuangLin/ANCOMBC", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "ancombc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc", - "Galaxy wrapper version": "1.4.0", - "Conda id": "bioconductor-ancombc", - "Conda version": "2.4.0", - "EDAM operation (no superclasses)": [ - "DNA barcoding" - ], - "EDAM topic (no superclasses)": [ - "Microbial ecology", - "Metagenomics", - "Taxonomy" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "anndata", - "Galaxy tool ids": [ - "anndata_export", - "anndata_import", - "anndata_inspect", - "anndata_manipulate", - "modify_loom" - ], - "Description": "Import, Export, Inspect and Manipulate Anndata and Loom objects", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://anndata.readthedocs.io", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "anndata", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata", - "Galaxy wrapper version": "0.10.3", - "Conda id": "anndata", - "Conda version": "0.6.22.post1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "annotatemyids", - "Galaxy tool ids": [ - "annotatemyids" - ], - "Description": "annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages", - "bio.tool id": "annotatemyids", - "bio.tool ids": [ - "annotatemyids" - ], - "biii": null, - "bio.tool name": "annotatemyids", - "bio.tool description": "This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.", - "EDAM operation": [ - "Annotation" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "annotatemyids", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids", - "Galaxy wrapper version": "3.18.0", - "Conda id": "bioconductor-org.hs.eg.db", - "Conda version": "3.18.0", - "EDAM operation (no superclasses)": [ - "Annotation" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "arriba", - "Galaxy tool ids": [ - "arriba", - "arriba_draw_fusions", - "arriba_get_filters" - ], - "Description": "Arriba detects fusion genes in RNA-Seq data after running RNA-STAR", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/suhrig/arriba", - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics" - ], - "ToolShed id": "arriba", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba", - "Galaxy wrapper version": "2.4.0", - "Conda id": "arriba", - "Conda version": "2.4.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "art", - "Galaxy tool ids": [ - "art_454", - "art_illumina", - "art_solid" - ], - "Description": "Simulator for Illumina, 454, and SOLiD sequencing data", - "bio.tool id": "art", - "bio.tool ids": [ - "art" - ], - "biii": null, - "bio.tool name": "ART", - "bio.tool description": "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD", - "EDAM operation": [ - "Conversion" - ], - "EDAM topic": [ - "Bioinformatics" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Data Source" - ], - "ToolShed id": "art", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/art", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/art", - "Galaxy wrapper version": "2014.11.03.0", - "Conda id": "art", - "Conda version": "2016.06.05", - "EDAM operation (no superclasses)": [ - "Conversion" - ], - "EDAM topic (no superclasses)": [ - "Bioinformatics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "artic", - "Galaxy tool ids": [ - "artic_guppyplex", - "artic_minion" - ], - "Description": "The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building", - "bio.tool id": "artic", - "bio.tool ids": [ - "artic" - ], - "biii": null, - "bio.tool name": "ARTIC", - "bio.tool description": "A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/artic-network/fieldbioinformatics", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic", - "Galaxy wrapper version": null, - "Conda id": "artic", - "Conda version": "1.2.4", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "assembly-stats", - "Galaxy tool ids": [ - "assembly_stats" - ], - "Description": "Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/rjchallis/assembly-stats", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "assembly_stats", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats", - "Galaxy wrapper version": "17.02", - "Conda id": "rjchallis-assembly-stats", - "Conda version": "17.02", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "augustus", - "Galaxy tool ids": [ - "augustus", - "augustus_training" - ], - "Description": "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.", - "bio.tool id": "augustus", - "bio.tool ids": [ - "augustus" - ], - "biii": null, - "bio.tool name": "AUGUSTUS", - "bio.tool description": "AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.", - "EDAM operation": [ - "Gene prediction", - "Ab-initio gene prediction", - "Homology-based gene prediction", - "Homology-based gene prediction", - "Operation" - ], - "EDAM topic": [ - "Gene transcripts", - "Gene and protein families" - ], - "Status": "To update", - "Source": "http://bioinf.uni-greifswald.de/augustus/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "augustus", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus", - "Galaxy wrapper version": "3.4.0", - "Conda id": "augustus", - "Conda version": "3.5.0", - "EDAM operation (no superclasses)": [ - "Ab-initio gene prediction", - "Homology-based gene prediction", - "Homology-based gene prediction", - "Operation" - ], - "EDAM topic (no superclasses)": [ - "Gene transcripts", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "b2btools", - "Galaxy tool ids": [ - "b2btools_single_sequence" - ], - "Description": "This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.", - "bio.tool id": "b2btools", - "bio.tool ids": [ - "b2btools" - ], - "biii": null, - "bio.tool name": "b2bTools", - "bio.tool description": "The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA", - "EDAM operation": [ - "Protein disorder prediction", - "Protein secondary structure prediction", - "Protein feature detection" - ], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bio2byte.be", - "ToolShed categories": [ - "Computational chemistry", - "Molecular Dynamics", - "Proteomics", - "Sequence Analysis", - "Synthetic Biology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools", - "Galaxy wrapper version": "3.0.5+galaxy0", - "Conda id": "b2btools", - "Conda version": "3.0.6", - "EDAM operation (no superclasses)": [ - "Protein disorder prediction", - "Protein secondary structure prediction" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bakta", - "Galaxy tool ids": [ - "bakta" - ], - "Description": "\"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.\"", - "bio.tool id": "bakta", - "bio.tool ids": [ - "bakta" - ], - "biii": null, - "bio.tool name": "Bakta", - "bio.tool description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Genomics", - "Data submission, annotation and curation", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/oschwengers/bakta", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bakta", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta", - "Galaxy wrapper version": "1.9.3", - "Conda id": "bakta", - "Conda version": "1.9.3", - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Data submission, annotation and curation", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bam_to_scidx", - "Galaxy tool ids": [ - "bam_to_scidx" - ], - "Description": "Contains a tool that converts a BAM file to an ScIdx file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "bam_to_scidx", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx", - "Galaxy wrapper version": "1.0.1", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bamutil", - "Galaxy tool ids": [ - "bamutil_clip_overlap", - "bamutil_diff" - ], - "Description": "bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/statgen/bamUtil", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bamutil", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil", - "Galaxy wrapper version": null, - "Conda id": "bamutil", - "Conda version": "1.0.15", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bandage", - "Galaxy tool ids": [ - "bandage_image", - "bandage_info" - ], - "Description": "Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily", - "bio.tool id": "bandage", - "bio.tool ids": [ - "bandage" - ], - "biii": null, - "bio.tool name": "Bandage", - "bio.tool description": "GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.", - "EDAM operation": [ - "Sequence assembly visualisation" - ], - "EDAM topic": [ - "Genomics", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/rrwick/Bandage", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "bandage", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage", - "Galaxy wrapper version": "2022.09", - "Conda id": "bandage_ng", - "Conda version": "2022.09", - "EDAM operation (no superclasses)": [ - "Sequence assembly visualisation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "barcode_splitter", - "Galaxy tool ids": [ - "barcode_splitter" - ], - "Description": "A utility to split sequence files using multiple sets of barcodes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/princeton_genomics/barcode_splitter/", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "barcode_splitter", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter", - "Galaxy wrapper version": "0.18.4.0", - "Conda id": "barcode_splitter", - "Conda version": "0.18.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "baredsc", - "Galaxy tool ids": [ - "baredsc_1d", - "baredsc_2d", - "baredsc_combine_1d", - "baredsc_combine_2d" - ], - "Description": "baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.", - "bio.tool id": "baredsc", - "bio.tool ids": [ - "baredsc" - ], - "biii": null, - "bio.tool name": "baredSC", - "bio.tool description": "The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.", - "EDAM operation": [ - "Data retrieval", - "Expression correlation analysis", - "Differential gene expression profiling" - ], - "EDAM topic": [ - "RNA-Seq", - "Cytometry", - "Transcriptomics", - "Gene transcripts", - "Statistics and probability" - ], - "Status": "Up-to-date", - "Source": "https://github.com/lldelisle/baredSC", - "ToolShed categories": [ - "Transcriptomics", - "Visualization" - ], - "ToolShed id": "baredsc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc", - "Galaxy wrapper version": "1.1.3", - "Conda id": "baredsc", - "Conda version": "1.1.3", - "EDAM operation (no superclasses)": [ - "Data retrieval", - "Expression correlation analysis", - "Differential gene expression profiling" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Cytometry", - "Transcriptomics", - "Gene transcripts", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "barrnap", - "Galaxy tool ids": [ - "barrnap" - ], - "Description": "Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.", - "bio.tool id": "barrnap", - "bio.tool ids": [ - "barrnap" - ], - "biii": null, - "bio.tool name": "Barrnap", - "bio.tool description": "Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).", - "EDAM operation": [ - "Gene prediction" - ], - "EDAM topic": [ - "Genomics", - "Model organisms", - "Model organisms" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "barrnap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap", - "Galaxy wrapper version": "1.2.2", - "Conda id": "barrnap", - "Conda version": "0.9", - "EDAM operation (no superclasses)": [ - "Gene prediction" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Model organisms", - "Model organisms" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "basil", - "Galaxy tool ids": [ - "basil" - ], - "Description": "Breakpoint detection, including large insertions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/seqan/anise_basil", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "basil", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil", - "Galaxy wrapper version": "1.2.0", - "Conda id": "anise_basil", - "Conda version": "1.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bax2bam", - "Galaxy tool ids": [ - "bax2bam" - ], - "Description": "BAX to BAM converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/pacificbiosciences/bax2bam/", - "ToolShed categories": [ - "Convert Formats", - "Sequence Analysis" - ], - "ToolShed id": "bax2bam", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam", - "Galaxy wrapper version": "0.0.11", - "Conda id": "bax2bam", - "Conda version": "0.0.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bayescan", - "Galaxy tool ids": [ - "BayeScan" - ], - "Description": "Detecting natural selection from population-based genetic data", - "bio.tool id": "bayescan", - "bio.tool ids": [ - "bayescan" - ], - "biii": null, - "bio.tool name": "BayeScan", - "bio.tool description": "BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.", - "EDAM operation": [ - "Statistical inference" - ], - "EDAM topic": [ - "Genetics", - "Evolutionary biology", - "Statistics and probability", - "DNA polymorphism" - ], - "Status": "To update", - "Source": "http://cmpg.unibe.ch/software/BayeScan/index.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bayescan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan", - "Galaxy wrapper version": "2.1", - "Conda id": "bayescan", - "Conda version": "2.0.1", - "EDAM operation (no superclasses)": [ - "Statistical inference" - ], - "EDAM topic (no superclasses)": [ - "Genetics", - "Evolutionary biology", - "Statistics and probability", - "DNA polymorphism" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bbtools", - "Galaxy tool ids": [ - "bbtools_bbduk", - "bbtools_bbmap", - "bbtools_bbmerge", - "bbtools_bbnorm", - "bbtools_callvariants", - "bbtools_tadpole" - ], - "Description": "BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.", - "bio.tool id": "bbmap", - "bio.tool ids": [ - "bbtools", - "bbmap" - ], - "biii": null, - "bio.tool name": "BBMap", - "bio.tool description": "BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.", - "EDAM operation": [ - "RNA-Seq analysis", - "Sequence trimming", - "Read mapping", - "Sequence contamination filtering", - "Read binning", - "Sequence alignment" - ], - "EDAM topic": [ - "Sequencing", - "RNA splicing", - "Whole genome sequencing", - "Phylogenetics", - "Metagenomics", - "RNA-Seq" - ], - "Status": "Up-to-date", - "Source": "https://jgi.doe.gov/data-and-tools/bbtools/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bbtools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools", - "Galaxy wrapper version": "39.06", - "Conda id": "bbmap", - "Conda version": "39.06", - "EDAM operation (no superclasses)": [ - "RNA-Seq analysis", - "Sequence trimming", - "Read mapping", - "Sequence contamination filtering", - "Read binning", - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "RNA splicing", - "Whole genome sequencing", - "Phylogenetics", - "Metagenomics", - "RNA-Seq" - ], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bcftools", - "Galaxy tool ids": [ - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@_from_vcf", - "bcftools_@EXECUTABLE@_to_vcf", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_plugin_@PLUGIN_ID@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@_list_samples", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@", - "bcftools_@EXECUTABLE@" - ], - "Description": "BCFtools toolkit wrappers", - "bio.tool id": "bcftools", - "bio.tool ids": [ - "bcftools" - ], - "biii": null, - "bio.tool name": "BCFtools", - "bio.tool description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.", - "EDAM operation": [ - "Data handling", - "Variant calling" - ], - "EDAM topic": [ - "Genetic variation", - "DNA polymorphism", - "GWAS study", - "Genotyping experiment" - ], - "Status": "To update", - "Source": "https://samtools.github.io/bcftools/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools", - "Galaxy wrapper version": "1.15.1", - "Conda id": "bcftools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [ - "Data handling", - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "DNA polymorphism", - "GWAS study", - "Genotyping experiment" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bctools", - "Galaxy tool ids": [ - "bctools_convert_to_binary_barcode", - "bctools_extract_crosslinked_nucleotides", - "bctools_extract_alignment_ends", - "bctools_extract_barcodes", - "bctools_merge_pcr_duplicates", - "bctools_remove_tail", - "bctools_remove_spurious_events" - ], - "Description": "bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/dmaticzka/bctools", - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools", - "Galaxy wrapper version": "0.2.2", - "Conda id": "bctools", - "Conda version": "0.2.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "beacon2", - "Galaxy tool ids": [ - "beacon2_csv2xlsx", - "beacon2_pxf2bff", - "beacon2_vcf2bff" - ], - "Description": "beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).", - "bio.tool id": "ga4gh_beacon", - "bio.tool ids": [ - "ga4gh_beacon" - ], - "biii": null, - "bio.tool name": "GA4GH Beacon", - "bio.tool description": "A global search engine for genetic mutations.", - "EDAM operation": [ - "Service discovery", - "Database search", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Genetic variation", - "Population genetics", - "Data security", - "Rare diseases" - ], - "Status": "Up-to-date", - "Source": "https://github.com/EGA-archive/beacon2-ri-tools/tree/main", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "beacon2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2", - "Galaxy wrapper version": "2.0.0", - "Conda id": "beacon2-ri-tools", - "Conda version": "2.0.0", - "EDAM operation (no superclasses)": [ - "Service discovery", - "Database search", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Genetic variation", - "Population genetics", - "Data security", - "Rare diseases" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "beagle", - "Galaxy tool ids": [ - "beagle" - ], - "Description": "Beagle is a program for phasing and imputing missing genotypes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://faculty.washington.edu/browning/beagle/beagle.html", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "beagle", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle", - "Galaxy wrapper version": "5.2_21Apr21.304", - "Conda id": "beagle", - "Conda version": "5.4_22Jul22.46e", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bedops", - "Galaxy tool ids": [ - "bedops-sort-bed" - ], - "Description": "BEDOPS: high-performance genomic feature operations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://bedops.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "bedops_sortbed", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://bedops.readthedocs.io/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops", - "Galaxy wrapper version": "2.4.41", - "Conda id": "bedops", - "Conda version": "2.4.41", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bedtools", - "Galaxy tool ids": [ - "bedtools_annotatebed", - "bedtools_bamtobed", - "bedtools_bed12tobed6", - "bedtools_bedtobam", - "bedtools_bedtoigv", - "bedtools_bedpetobam", - "bedtools_closestbed", - "bedtools_clusterbed", - "bedtools_complementbed", - "bedtools_coveragebed", - "bedtools_expandbed", - "bedtools_fisher", - "bedtools_flankbed", - "bedtools_genomecoveragebed", - "bedtools_getfastabed", - "bedtools_groupbybed", - "bedtools_intersectbed", - "bedtools_jaccard", - "bedtools_links", - "bedtools_makewindowsbed", - "bedtools_map", - "bedtools_maskfastabed", - "bedtools_mergebed", - "bedtools_multicovtbed", - "bedtools_multiintersectbed", - "bedtools_nucbed", - "bedtools_overlapbed", - "bedtools_randombed", - "bedtools_reldistbed", - "bedtools_shufflebed", - "bedtools_slopbed", - "bedtools_sortbed", - "bedtools_spacingbed", - "bedtools_subtractbed", - "bedtools_tagbed", - "bedtools_unionbedgraph", - "bedtools_windowbed" - ], - "Description": "bedtools is a powerful toolset for genome arithmetic", - "bio.tool id": "bedtools", - "bio.tool ids": [ - "bedtools" - ], - "biii": null, - "bio.tool name": "BEDTools", - "bio.tool description": "BEDTools is an extensive suite of utilities for comparing genomic features in BED format.", - "EDAM operation": [ - "Mapping" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/arq5x/bedtools2", - "ToolShed categories": [ - "Genomic Interval Operations", - "Text Manipulation" - ], - "ToolShed id": "bedtools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools", - "Galaxy wrapper version": "2.31.1", - "Conda id": "bedtools", - "Conda version": "2.31.1", - "EDAM operation (no superclasses)": [ - "Mapping" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 37, - "Available on UseGalaxy.org.au": 37, - "Available on UseGalaxy.eu": 37, - "Available on UseGalaxy.org.fr": 37 - }, - { - "Galaxy wrapper id": "bellerophon", - "Galaxy tool ids": [ - "bellerophon" - ], - "Description": "Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/davebx/bellerophon", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bellerophon", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/davebx/bellerophon", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon", - "Galaxy wrapper version": "1.0", - "Conda id": "bellerophon", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "berokka", - "Galaxy tool ids": [ - "berokka" - ], - "Description": "Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/tseemann/berokka", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "berokka", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka", - "Galaxy wrapper version": "0.2.3", - "Conda id": "berokka", - "Conda version": "0.2.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bigscape", - "Galaxy tool ids": [ - "bigscape" - ], - "Description": "Construct sequence similarity networks of BGCs and groups them into GCF", - "bio.tool id": "BiG-SCAPE", - "bio.tool ids": [ - "BiG-SCAPE" - ], - "biii": null, - "bio.tool name": "BiG-SCAPE", - "bio.tool description": "A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.", - "EDAM operation": [ - "Clustering", - "Global alignment", - "Fold recognition" - ], - "EDAM topic": [ - "Phylogeny", - "Microbial ecology", - "Mapping", - "Metabolomics", - "Bioinformatics", - "Gene and protein families" - ], - "Status": "Up-to-date", - "Source": "https://github.com/medema-group/BiG-SCAPE", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "bigscape", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape", - "Galaxy wrapper version": "1.1.9", - "Conda id": "bigscape", - "Conda version": "1.1.9", - "EDAM operation (no superclasses)": [ - "Clustering", - "Global alignment", - "Fold recognition" - ], - "EDAM topic (no superclasses)": [ - "Phylogeny", - "Microbial ecology", - "Mapping", - "Metabolomics", - "Bioinformatics", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "binning_refiner", - "Galaxy tool ids": [ - "bin_refiner" - ], - "Description": "Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.", - "bio.tool id": "binning_refiner", - "bio.tool ids": [ - "binning_refiner" - ], - "biii": null, - "bio.tool name": "Binning_refiner", - "bio.tool description": "Improving genome bins through the combination of different binning programs", - "EDAM operation": [ - "Read binning", - "Sequence clustering" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence assembly", - "Microbial ecology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/songweizhi/Binning_refiner", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "binning_refiner", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner", - "Galaxy wrapper version": "1.4.3", - "Conda id": "binning_refiner", - "Conda version": "1.4.3", - "EDAM operation (no superclasses)": [ - "Read binning", - "Sequence clustering" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence assembly", - "Microbial ecology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bioext", - "Galaxy tool ids": [ - "bioext_bam2msa", - "bioext_bealign" - ], - "Description": "A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pypi.python.org/pypi/biopython-extensions/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/davebx/bioext-gx/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext", - "Galaxy wrapper version": "0.21.2", - "Conda id": "python-bioext", - "Conda version": "0.21.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bioinformatics_cafe", - "Galaxy tool ids": [ - "fasta_regex_finder" - ], - "Description": "Miscellanea of scripts for bioinformatics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/dariober/bioinformatics-cafe/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bioinformatics_cafe", - "Galaxy wrapper owner": "mbernt", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe", - "Galaxy wrapper version": "0.1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biom_format", - "Galaxy tool ids": [ - "biom_add_metadata", - "biom_convert", - "biom_from_uc", - "biom_normalize_table", - "biom_subset_table", - "biom_summarize_table" - ], - "Description": "The biom-format package provides a command line interface and Python API for working with BIOM files.", - "bio.tool id": "biomformat", - "bio.tool ids": [ - "biomformat" - ], - "biii": null, - "bio.tool name": "biomformat", - "bio.tool description": "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly \"R flavor\" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.", - "EDAM operation": [ - "Formatting" - ], - "EDAM topic": [ - "Laboratory information management", - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/biocore/biom-format", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format", - "Galaxy wrapper version": "2.1.15", - "Conda id": "biom-format", - "Conda version": "2.1.7", - "EDAM operation (no superclasses)": [ - "Formatting" - ], - "EDAM topic (no superclasses)": [ - "Laboratory information management", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bioperl", - "Galaxy tool ids": [ - "bp_genbank2gff3" - ], - "Description": "Converts GenBank format files to GFF3", - "bio.tool id": "bioperl", - "bio.tool ids": [ - "bioperl" - ], - "biii": null, - "bio.tool name": "BioPerl", - "bio.tool description": "A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.", - "EDAM operation": [ - "Data handling", - "Service invocation" - ], - "EDAM topic": [ - "Genomics", - "Software engineering", - "Data management" - ], - "Status": "To update", - "Source": "https://bioperl.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bp_genbank2gff3", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl", - "Galaxy wrapper version": "1.1", - "Conda id": "perl-bioperl", - "Conda version": "1.7.8", - "EDAM operation (no superclasses)": [ - "Data handling", - "Service invocation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Software engineering" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "biscot", - "Galaxy tool ids": [ - "biscot" - ], - "Description": "Bionano scaffolding correction tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/institut-de-genomique/biscot", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "biscot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/bgruening/iuc/tree/master/tools/biscot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot", - "Galaxy wrapper version": "2.3.3", - "Conda id": "biscot", - "Conda version": "2.3.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast", - "Galaxy tool ids": [ - "magicblast" - ], - "Description": "Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://ncbi.github.io/magicblast/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "magicblast", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast", - "Galaxy wrapper version": "1.7.0", - "Conda id": "magicblast", - "Conda version": "1.7.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blastxml_to_gapped_gff3", - "Galaxy tool ids": [ - "blastxml_to_gapped_gff3" - ], - "Description": "BlastXML to gapped GFF3", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats", - "Sequence Analysis" - ], - "ToolShed id": "blastxml_to_gapped_gff3", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3", - "Galaxy wrapper version": "1.1", - "Conda id": "bcbiogff", - "Conda version": "0.6.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bowtie2", - "Galaxy tool ids": [ - "bowtie2" - ], - "Description": "Bowtie2: Fast and sensitive read alignment", - "bio.tool id": "bowtie2", - "bio.tool ids": [ - "bowtie2" - ], - "biii": null, - "bio.tool name": "Bowtie 2", - "bio.tool description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.", - "EDAM operation": [ - "Read mapping" - ], - "EDAM topic": [ - "Mapping", - "Genomics", - "Mapping" - ], - "Status": "To update", - "Source": "http://bowtie-bio.sourceforge.net/bowtie2", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "bowtie2", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2", - "Galaxy wrapper version": "2.5.3", - "Conda id": "bowtie2", - "Conda version": "2.5.4", - "EDAM operation (no superclasses)": [ - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Mapping", - "Genomics", - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bracken", - "Galaxy tool ids": [ - "est_abundance" - ], - "Description": "Bayesian Reestimation of Abundance with KrakEN", - "bio.tool id": "bracken", - "bio.tool ids": [ - "bracken" - ], - "biii": null, - "bio.tool name": "Bracken", - "bio.tool description": "Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", - "EDAM operation": [ - "Statistical calculation" - ], - "EDAM topic": [ - "Metagenomics", - "Microbial ecology" - ], - "Status": "Up-to-date", - "Source": "https://ccb.jhu.edu/software/bracken/", - "ToolShed categories": [ - "Sequence Analysis", - "Metagenomics" - ], - "ToolShed id": "bracken", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken", - "Galaxy wrapper version": "2.9", - "Conda id": "bracken", - "Conda version": "2.9", - "EDAM operation (no superclasses)": [ - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbial ecology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "breseq", - "Galaxy tool ids": [ - "breseq" - ], - "Description": "Predicts mutations in microbial genomes", - "bio.tool id": "breseq", - "bio.tool ids": [ - "breseq" - ], - "biii": null, - "bio.tool name": "breseq", - "bio.tool description": "Runs Breseq software on a set of fastq files.", - "EDAM operation": [ - "Polymorphism detection" - ], - "EDAM topic": [ - "Sequencing", - "Sequence analysis", - "DNA mutation" - ], - "Status": "To update", - "Source": "https://github.com/barricklab/breseq", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "breseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq", - "Galaxy wrapper version": "0.35.5", - "Conda id": "breseq", - "Conda version": "0.38.3", - "EDAM operation (no superclasses)": [ - "Polymorphism detection" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence analysis", - "DNA mutation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "busco", - "Galaxy tool ids": [ - "busco" - ], - "Description": "BUSCO assess genome and annotation completeness", - "bio.tool id": "busco", - "bio.tool ids": [ - "busco" - ], - "biii": null, - "bio.tool name": "BUSCO", - "bio.tool description": "Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", - "EDAM operation": [ - "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Genomics", - "Transcriptomics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://gitlab.com/ezlab/busco/-/releases", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "busco", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco", - "Galaxy wrapper version": "5.5.0", - "Conda id": "busco", - "Conda version": "5.7.1", - "EDAM operation (no superclasses)": [ - "Sequence assembly validation", - "Scaffolding", - "Genome assembly", - "Transcriptome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Transcriptomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bwa", - "Galaxy tool ids": [ - "bwa_mem", - "bwa" - ], - "Description": "Wrapper for bwa mem, aln, sampe, and samse", - "bio.tool id": "bwa", - "bio.tool ids": [ - "bwa" - ], - "biii": null, - "bio.tool name": "BWA", - "bio.tool description": "Fast, accurate, memory-efficient aligner for short and long sequencing reads", - "EDAM operation": [ - "Genome indexing", - "Sequence alignment", - "Read mapping", - "Sequence alignment", - "Generation", - "Sequence alignment", - "Generation", - "Sequence alignment", - "Sequence alignment" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "http://bio-bwa.sourceforge.net/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "bwa", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa", - "Galaxy wrapper version": "0.7.18", - "Conda id": "bwa", - "Conda version": "0.7.18", - "EDAM operation (no superclasses)": [ - "Genome indexing", - "Sequence alignment", - "Read mapping", - "Sequence alignment", - "Generation", - "Sequence alignment", - "Generation", - "Sequence alignment", - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "bwa_mem2", - "Galaxy tool ids": [ - "bwa_mem2" - ], - "Description": "Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.", - "bio.tool id": "bwa-mem2", - "bio.tool ids": [ - "bwa-mem2" - ], - "biii": null, - "bio.tool name": "Bwa-mem2", - "bio.tool description": "Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/bwa-mem2/bwa-mem2", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "bwa_mem2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2", - "Galaxy wrapper version": "2.2.1", - "Conda id": "bwa-mem2", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bwameth", - "Galaxy tool ids": [ - "bwameth" - ], - "Description": "Fast and accurate alignment of BS-seq reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/brentp/bwa-meth", - "ToolShed categories": [ - "Sequence Analysis", - "Next Gen Mappers" - ], - "ToolShed id": "bwameth", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth", - "Galaxy wrapper version": "0.2.7", - "Conda id": "bwameth", - "Conda version": "0.2.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cactus", - "Galaxy tool ids": [ - "cactus_cactus", - "cactus_export" - ], - "Description": "Cactus is a reference-free whole-genome multiple alignment program", - "bio.tool id": "cactus", - "bio.tool ids": [ - "cactus" - ], - "biii": null, - "bio.tool name": "Cactus", - "bio.tool description": "Cactus is a reference-free whole-genome multiple alignment program.", - "EDAM operation": [ - "Multiple sequence alignment", - "Genome alignment" - ], - "EDAM topic": [ - "Genomics", - "Sequence analysis", - "Phylogeny", - "Sequence assembly", - "Mapping", - "Phylogenetics" - ], - "Status": "To update", - "Source": "https://github.com/ComparativeGenomicsToolkit/cactus", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "cactus", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus", - "Galaxy wrapper version": "2.7.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Multiple sequence alignment", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly", - "Mapping", - "Phylogenetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "calculate_contrast_threshold", - "Galaxy tool ids": [ - "calculate_contrast_threshold" - ], - "Description": "Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold", - "ToolShed categories": [ - "Visualization", - "Genomic Interval Operations", - "SAM" - ], - "ToolShed id": "calculate_contrast_threshold", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold", - "Galaxy wrapper version": "1.0.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "calculate_numeric_param", - "Galaxy tool ids": [ - "calculate_numeric_param" - ], - "Description": "Calculate a numeric parameter value using integer and float values.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "calculate_numeric_param", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param", - "Galaxy wrapper version": "0.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cami_amber", - "Galaxy tool ids": [ - "cami_amber", - "cami_amber_add", - "cami_amber_convert" - ], - "Description": "Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/CAMI-challenge/AMBER", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "cami_amber", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber", - "Galaxy wrapper version": "2.0.4", - "Conda id": "cami-amber", - "Conda version": "2.0.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cat", - "Galaxy tool ids": [ - "cat_add_names", - "cat_bins", - "cat_contigs", - "cat_prepare", - "cat_summarise" - ], - "Description": "Contig Annotation Tool (CAT)", - "bio.tool id": "cat_bins", - "bio.tool ids": [ - "cat_bins" - ], - "biii": null, - "bio.tool name": "CAT and BAT", - "bio.tool description": "Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.", - "EDAM operation": [ - "Taxonomic classification", - "Sequence assembly", - "Coding region prediction" - ], - "EDAM topic": [ - "Metagenomics", - "Metagenomic sequencing", - "Taxonomy", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/dutilh/CAT", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "contig_annotation_tool", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat", - "Galaxy wrapper version": "5.2.3", - "Conda id": "cat", - "Conda version": "5.3", - "EDAM operation (no superclasses)": [ - "Taxonomic classification", - "Sequence assembly", - "Coding region prediction" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Metagenomic sequencing", - "Taxonomy", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cdhit", - "Galaxy tool ids": [ - "cd_hit" - ], - "Description": "Cluster or compare biological sequence datasets", - "bio.tool id": "cd-hit", - "bio.tool ids": [ - "cd-hit" - ], - "biii": null, - "bio.tool name": "cd-hit", - "bio.tool description": "Cluster a nucleotide dataset into representative sequences.", - "EDAM operation": [ - "Sequence clustering" - ], - "EDAM topic": [ - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "http://weizhongli-lab.org/cd-hit/", - "ToolShed categories": [ - "Sequence Analysis", - "Fasta Manipulation" - ], - "ToolShed id": "cd_hit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit", - "Galaxy wrapper version": "4.8.1", - "Conda id": "cd-hit", - "Conda version": "4.8.1", - "EDAM operation (no superclasses)": [ - "Sequence clustering" - ], - "EDAM topic (no superclasses)": [ - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cemitool", - "Galaxy tool ids": [ - "cemitool" - ], - "Description": "Gene co-expression network analysis tool", - "bio.tool id": "cemitool", - "bio.tool ids": [ - "cemitool" - ], - "biii": null, - "bio.tool name": "CEMiTool", - "bio.tool description": "It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.", - "EDAM operation": [ - "Enrichment analysis", - "Pathway or network analysis" - ], - "EDAM topic": [ - "Gene expression", - "Transcriptomics", - "Microarray experiment" - ], - "Status": "To update", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "cemitool", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool", - "Galaxy wrapper version": "1.18.1", - "Conda id": "bioconductor-cemitool", - "Conda version": "1.26.0", - "EDAM operation (no superclasses)": [ - "Enrichment analysis", - "Pathway or network analysis" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Microarray experiment" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "charts", - "Galaxy tool ids": [ - "charts" - ], - "Description": "Enables advanced visualization options in Galaxy Charts", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "charts", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts", - "Galaxy wrapper version": "1.0.1", - "Conda id": "r-getopt", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "checkm", - "Galaxy tool ids": [ - "checkm_analyze", - "checkm_lineage_set", - "checkm_lineage_wf", - "checkm_plot", - "checkm_qa", - "checkm_taxon_set", - "checkm_taxonomy_wf", - "checkm_tetra", - "checkm_tree", - "checkm_tree_qa" - ], - "Description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes", - "bio.tool id": "checkm", - "bio.tool ids": [ - "checkm" - ], - "biii": null, - "bio.tool name": "CheckM", - "bio.tool description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.", - "EDAM operation": [ - "Sequence assembly validation", - "Validation", - "Sequence composition calculation", - "Sequencing quality control", - "Statistical calculation" - ], - "EDAM topic": [ - "Genomics", - "Phylogenomics", - "Phylogenetics", - "Taxonomy", - "Metagenomics", - "Data quality management" - ], - "Status": "To update", - "Source": "https://github.com/Ecogenomics/CheckM", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "checkm", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm", - "Galaxy wrapper version": "1.2.0", - "Conda id": "checkm-genome", - "Conda version": "1.2.2", - "EDAM operation (no superclasses)": [ - "Sequence assembly validation", - "Sequence composition calculation", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Phylogenomics", - "Phylogenetics", - "Taxonomy", - "Metagenomics", - "Data quality management" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 10 - }, - { - "Galaxy wrapper id": "cherri", - "Galaxy tool ids": [ - "cherri_eval", - "cherri_train" - ], - "Description": "Computational Help Evaluating RNA-RNA interactions", - "bio.tool id": "cherri", - "bio.tool ids": [ - "cherri" - ], - "biii": null, - "bio.tool name": "cherri", - "bio.tool description": "CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.", - "EDAM operation": [], - "EDAM topic": [ - "Molecular interactions, pathways and networks", - "Structure analysis", - "Machine learning" - ], - "Status": "To update", - "Source": "https://github.com/BackofenLab/Cherri", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri", - "Galaxy wrapper version": "0.7", - "Conda id": "cherri", - "Conda version": "0.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Molecular interactions, pathways and networks", - "Structure analysis", - "Machine learning" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chewbbaca", - "Galaxy tool ids": [ - "chewbbaca_allelecall", - "chewbbaca_allelecallevaluator", - "chewbbaca_createschema", - "chewbbaca_downloadschema", - "chewbbaca_extractcgmlst", - "chewbbaca_joinprofiles", - "chewbbaca_nsstats", - "chewbbaca_prepexternalschema" - ], - "Description": "BSR-Based Allele Calling Algorithm", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/B-UMMI/chewBBACA/tree/master", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "chewbbaca", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca", - "Galaxy wrapper version": null, - "Conda id": "chewbbaca", - "Conda version": "3.3.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chira", - "Galaxy tool ids": [ - "chira_collapse", - "chira_extract", - "chira_map", - "chira_merge", - "chira_quantify" - ], - "Description": "Chimeric Read Annotator for RNA-RNA interactome data", - "bio.tool id": "chira", - "bio.tool ids": [ - "chira" - ], - "biii": null, - "bio.tool name": "ChiRA", - "bio.tool description": "ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.", - "EDAM operation": [], - "EDAM topic": [ - "RNA", - "Molecular interactions, pathways and networks", - "Functional, regulatory and non-coding RNA" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pavanvidem/chira", - "ToolShed categories": [ - "RNA", - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "chira", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira", - "Galaxy wrapper version": "1.4.3", - "Conda id": "chira", - "Conda version": "1.4.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Molecular interactions, pathways and networks", - "Functional, regulatory and non-coding RNA" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chopin2", - "Galaxy tool ids": [ - "chopin2" - ], - "Description": "Domain-Agnostic Supervised Learning with Hyperdimensional Computing", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/cumbof/chopin2", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "chopin2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2", - "Galaxy wrapper version": "1.0.8.post1", - "Conda id": "chopin2", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "chromeister", - "Galaxy tool ids": [ - "chromeister" - ], - "Description": "ultra-fast pairwise genome comparisons", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/estebanpw/chromeister", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "chromeister", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister", - "Galaxy wrapper version": "1.5.a", - "Conda id": "chromeister", - "Conda version": "1.5.a", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "circexplorer2", - "Galaxy tool ids": [ - "circexplorer2" - ], - "Description": "Comprehensive and integrative circular RNA analysis toolset.", - "bio.tool id": "circexplorer2", - "bio.tool ids": [ - "circexplorer2" - ], - "biii": null, - "bio.tool name": "CIRCexplorer2", - "bio.tool description": "Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.", - "EDAM operation": [], - "EDAM topic": [ - "RNA splicing", - "Gene transcripts", - "Literature and language" - ], - "Status": "Up-to-date", - "Source": "https://github.com/YangLab/CIRCexplorer2", - "ToolShed categories": [ - "RNA", - "Assembly" - ], - "ToolShed id": "circexplorer2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2", - "Galaxy wrapper version": "2.3.8", - "Conda id": "circexplorer2", - "Conda version": "2.3.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "RNA splicing", - "Gene transcripts", - "Literature and language" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "circos", - "Galaxy tool ids": [ - "circos_aln_to_links", - "circos_binlinks", - "circos_bundlelinks", - "circos", - "circos_gc_skew", - "circos_resample", - "circos_wiggle_to_scatter", - "circos_wiggle_to_stacked", - "circos_tableviewer", - "circos_interval_to_text", - "circos_interval_to_tile" - ], - "Description": "Build Circos Plots in Galaxy", - "bio.tool id": "galactic_circos", - "bio.tool ids": [ - "galactic_circos" - ], - "biii": null, - "bio.tool name": "Galactic Circos", - "bio.tool description": "Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.", - "EDAM operation": [ - "Sequence visualisation" - ], - "EDAM topic": [], - "Status": "To update", - "Source": "http://circos.ca/", - "ToolShed categories": [ - "Graphics" - ], - "ToolShed id": "circos", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos", - "Galaxy wrapper version": "0.69.8", - "Conda id": "circos", - "Conda version": "0.69.9", - "EDAM operation (no superclasses)": [ - "Sequence visualisation" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 11, - "Available on UseGalaxy.org.au": 11, - "Available on UseGalaxy.eu": 11, - "Available on UseGalaxy.org.fr": 11 - }, - { - "Galaxy wrapper id": "cite_seq_count", - "Galaxy tool ids": [ - "cite_seq_count" - ], - "Description": "Count CMO/HTO", - "bio.tool id": "CITE-seq-Count", - "bio.tool ids": [ - "CITE-seq-Count" - ], - "biii": null, - "bio.tool name": "CITE-seq-Count", - "bio.tool description": "Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.", - "EDAM operation": [ - "RNA-Seq quantification" - ], - "EDAM topic": [ - "Transcriptomics", - "Immunoproteins and antigens" - ], - "Status": "Up-to-date", - "Source": "https://github.com/Hoohm/CITE-seq-Count", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cite_seq_count", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count", - "Galaxy wrapper version": "1.4.4", - "Conda id": "cite-seq-count", - "Conda version": "1.4.4", - "EDAM operation (no superclasses)": [ - "RNA-Seq quantification" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Immunoproteins and antigens" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "clair3", - "Galaxy tool ids": [ - "clair3" - ], - "Description": "Symphonizing pileup and full-alignment for high-performance long-read variant calling", - "bio.tool id": "clair3", - "bio.tool ids": [ - "clair3" - ], - "biii": null, - "bio.tool name": "Clair3", - "bio.tool description": "Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.", - "EDAM operation": [ - "Variant calling" - ], - "EDAM topic": [ - "Molecular genetics" - ], - "Status": "To update", - "Source": "https://github.com/HKU-BAL/Clair3", - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "clair3", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3", - "Galaxy wrapper version": "0.1.12", - "Conda id": "clair3", - "Conda version": "1.0.8", - "EDAM operation (no superclasses)": [ - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Molecular genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "clustalw", - "Galaxy tool ids": [ - "clustalw" - ], - "Description": "ClustalW multiple sequence alignment program for DNA or proteins", - "bio.tool id": "clustal2", - "bio.tool ids": [ - "clustal2" - ], - "biii": null, - "bio.tool name": "Clustal 2 (Clustal W, Clustal X)", - "bio.tool description": "Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.", - "EDAM operation": [ - "Multiple sequence alignment" - ], - "EDAM topic": [ - "Phylogeny", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "http://www.clustal.org/clustal2/", - "ToolShed categories": [ - "Phylogenetics", - "Sequence Analysis" - ], - "ToolShed id": "clustalw", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw", - "Galaxy wrapper version": "2.1", - "Conda id": "clustalw", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [ - "Multiple sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Phylogeny", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cnv-phenopacket", - "Galaxy tool ids": [ - "cnv_phenopacket" - ], - "Description": "cnv-phenopacket Converts TSV metadata file to JSON.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pypi.org/project/cnv-phenopacket/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "cnv_phenopacket", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket", - "Galaxy wrapper version": "1.0.2", - "Conda id": "cnv-phenopacket", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cnv-vcf2json", - "Galaxy tool ids": [ - "cnv_vcf2json" - ], - "Description": "cnv-vcf2json Converts structural variants VCF file to JSON.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pypi.org/project/cnv-phenopacket/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "cnv-vcf2json", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json", - "Galaxy wrapper version": "1.0.4", - "Conda id": "cnv-vcf2json", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cnvkit", - "Galaxy tool ids": [ - "cnvkit_access", - "cnvkit_antitarget", - "cnvkit_autobin", - "cnvkit_batch", - "cnvkit_breaks", - "cnvkit_call", - "cnvkit_coverage", - "cnvkit_diagram", - "cnvkit_fix", - "cnvkit_genemetrics", - "cnvkit_heatmap", - "cnvkit_reference", - "cnvkit_scatter", - "cnvkit_segment", - "cnvkit_segmetrics", - "cnvkit_sex", - "cnvkit_target" - ], - "Description": "detecting copy number variants and alterations genome-wide from high-throughput sequencing", - "bio.tool id": "cnvkit", - "bio.tool ids": [ - "cnvkit" - ], - "biii": null, - "bio.tool name": "CNVkit", - "bio.tool description": "CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.", - "EDAM operation": [ - "Variant calling" - ], - "EDAM topic": [ - "DNA structural variation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/etal/cnvkit", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "cnvkit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit", - "Galaxy wrapper version": "0.9.11", - "Conda id": "cnvkit", - "Conda version": "0.9.11", - "EDAM operation (no superclasses)": [ - "Variant calling" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 17, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "codeml", - "Galaxy tool ids": [ - "codeml" - ], - "Description": "Detects positive selection", - "bio.tool id": "paml", - "bio.tool ids": [ - "paml" - ], - "biii": null, - "bio.tool name": "PAML", - "bio.tool description": "Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.", - "EDAM operation": [ - "Probabilistic sequence generation", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", - "Phylogenetic tree analysis" - ], - "EDAM topic": [ - "Phylogenetics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://abacus.gene.ucl.ac.uk/software/paml.html", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "codeml", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml", - "Galaxy wrapper version": "4.9", - "Conda id": "paml", - "Conda version": "4.10.7", - "EDAM operation (no superclasses)": [ - "Probabilistic sequence generation" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cojac", - "Galaxy tool ids": [ - "cooc_mutbamscan", - "cooc_pubmut", - "cooc_tabmut" - ], - "Description": "co-occurrence of mutations on amplicons", - "bio.tool id": "cojac", - "bio.tool ids": [ - "cojac" - ], - "biii": null, - "bio.tool name": "COJAC", - "bio.tool description": "CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.", - "EDAM operation": [], - "EDAM topic": [ - "Genetic variation" - ], - "Status": "To update", - "Source": "https://github.com/cbg-ethz/cojac", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": "cojac", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac", - "Galaxy wrapper version": "0.9.1", - "Conda id": "cojac", - "Conda version": "0.9.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Genetic variation" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "colabfold", - "Galaxy tool ids": [ - "colabfold_alphafold", - "colabfold_msa" - ], - "Description": "Protein prediction based on AlphaFold2", - "bio.tool id": "Colabfold", - "bio.tool ids": [ - "Colabfold" - ], - "biii": null, - "bio.tool name": "ColabFold", - "bio.tool description": "ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.", - "EDAM operation": [ - "Database search", - "Protein structure prediction", - "Fold recognition" - ], - "EDAM topic": [ - "Protein folds and structural domains", - "Protein folding, stability and design", - "Structure prediction", - "Sequence sites, features and motifs", - "Metagenomics" - ], - "Status": "To update", - "Source": "https://github.com/sokrypton/ColabFold", - "ToolShed categories": [ - "Proteomics", - "Graphics" - ], - "ToolShed id": "colabfold", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/sokrypton/ColabFold", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold", - "Galaxy wrapper version": "1.5.5", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Database search", - "Protein structure prediction", - "Fold recognition" - ], - "EDAM topic (no superclasses)": [ - "Protein folds and structural domains", - "Protein folding, stability and design", - "Structure prediction", - "Sequence sites, features and motifs", - "Metagenomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "colibread", - "Galaxy tool ids": [ - "commet", - "discosnp_rad", - "discosnp_pp", - "kissplice", - "lordec", - "mapsembler2", - "takeabreak" - ], - "Description": "Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://colibread.inria.fr/", - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "colibread", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread", - "Galaxy wrapper version": "24.7.14+galaxy0", - "Conda id": "commet", - "Conda version": "24.7.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "collection_column_join", - "Galaxy tool ids": [ - "collection_column_join" - ], - "Description": "Column Join on Collections", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "collection_column_join", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join", - "Galaxy wrapper version": "0.0.3", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "collection_element_identifiers", - "Galaxy tool ids": [ - "collection_element_identifiers" - ], - "Description": "Extract element identifiers of a collection", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "collection_element_identifiers", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers", - "Galaxy wrapper version": "0.0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "column_maker", - "Galaxy tool ids": [ - "Add_a_column1" - ], - "Description": "Compute an expression on every row", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "column_maker", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker", - "Galaxy wrapper version": "2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "column_order_header_sort", - "Galaxy tool ids": [ - "column_order_header_sort" - ], - "Description": "Sort Column Order by heading", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "column_order_header_sort", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort", - "Galaxy wrapper version": "0.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "column_remove_by_header", - "Galaxy tool ids": [ - "column_remove_by_header" - ], - "Description": "Remove columns by header", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "column_remove_by_header", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header", - "Galaxy wrapper version": "1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "compleasm", - "Galaxy tool ids": [ - "compleasm" - ], - "Description": "Compleasm: a faster and more accurate reimplementation of BUSCO", - "bio.tool id": "compleasm", - "bio.tool ids": [ - "compleasm" - ], - "biii": null, - "bio.tool name": "compleasm", - "bio.tool description": "\"Compleasm: a faster and more accurate reimplementation of BUSCO\"", - "EDAM operation": [ - "Sequence assembly validation", - "Sequence analysis", - "Scaffolding", - "Transcriptome assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Genomics", - "Transcriptomics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/huangnengCSU/compleasm", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "compleasm", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm", - "Galaxy wrapper version": "0.2.6", - "Conda id": "compleasm", - "Conda version": "0.2.6", - "EDAM operation (no superclasses)": [ - "Sequence assembly validation", - "Sequence analysis", - "Scaffolding", - "Transcriptome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Transcriptomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "compose_text_param", - "Galaxy tool ids": [ - "compose_text_param" - ], - "Description": "Compose a text parameter value using text, integer and float values", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "compose_text_param", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param", - "Galaxy wrapper version": "0.1.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "compress_file", - "Galaxy tool ids": [ - "compress_file" - ], - "Description": "Compress files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "compress_file", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file", - "Galaxy wrapper version": "0.1.0", - "Conda id": "gzip", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "concoct", - "Galaxy tool ids": [ - "concoct", - "concoct_coverage_table", - "concoct_cut_up_fasta", - "concoct_extract_fasta_bins", - "concoct_merge_cut_up_clustering" - ], - "Description": "CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.", - "bio.tool id": "concoct", - "bio.tool ids": [ - "concoct" - ], - "biii": null, - "bio.tool name": "CONCOCT", - "bio.tool description": "A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.", - "EDAM operation": [ - "Sequence clustering", - "Read binning" - ], - "EDAM topic": [ - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/BinPro/CONCOCT", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "concoct", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct", - "Galaxy wrapper version": "1.1.0", - "Conda id": "concoct", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [ - "Sequence clustering", - "Read binning" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "cosg", - "Galaxy tool ids": [ - "cosg" - ], - "Description": "Marker gene identification for single-cell sequencing data using COSG.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/genecell/COSG", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "cosg", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg", - "Galaxy wrapper version": "1.0.1", - "Conda id": "cosg", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "coverage_report", - "Galaxy tool ids": [ - "CoverageReport2" - ], - "Description": "Generate Detailed Coverage Report from BAM file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "coverage_report", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report", - "Galaxy wrapper version": "0.0.4", - "Conda id": "perl-number-format", - "Conda version": "1.76", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "coverm", - "Galaxy tool ids": [ - "coverm_contig", - "coverm_genome" - ], - "Description": "CoverM genome and contig wrappers", - "bio.tool id": "coverm", - "bio.tool ids": [ - "coverm" - ], - "biii": null, - "bio.tool name": "CoverM", - "bio.tool description": "Read coverage calculator for metagenomics", - "EDAM operation": [ - "Local alignment" - ], - "EDAM topic": [ - "Bioinformatics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/wwood/CoverM", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "coverm", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/coverm", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm", - "Galaxy wrapper version": "0.7.0", - "Conda id": "coverm", - "Conda version": "0.7.0", - "EDAM operation (no superclasses)": [ - "Local alignment" - ], - "EDAM topic (no superclasses)": [ - "Bioinformatics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "crispr_studio", - "Galaxy tool ids": [ - "crispr_studio" - ], - "Description": "CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.", - "bio.tool id": "crisprstudio", - "bio.tool ids": [ - "crisprstudio" - ], - "biii": null, - "bio.tool name": "CRISPRStudio", - "bio.tool description": "CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.", - "EDAM operation": [ - "Visualisation" - ], - "EDAM topic": [ - "Sequence analysis", - "Genomics", - "Data visualisation" - ], - "Status": "To update", - "Source": "https://github.com/moineaulab/CRISPRStudio", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "crispr_studio", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio", - "Galaxy wrapper version": "1+galaxy0", - "Conda id": "crispr_studio", - "Conda version": "1", - "EDAM operation (no superclasses)": [ - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Genomics", - "Data visualisation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "crosscontamination_barcode_filter", - "Galaxy tool ids": [ - "crosscontamination_barcode_filter" - ], - "Description": "Barcode contamination discovery tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "Visualization" - ], - "ToolShed id": "crosscontamination_barcode_filter", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter", - "Galaxy wrapper version": "0.3", - "Conda id": "r-ggplot2", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "crossmap", - "Galaxy tool ids": [ - "crossmap_bam", - "crossmap_bed", - "crossmap_bw", - "crossmap_gff", - "crossmap_region", - "crossmap_vcf", - "crossmap_wig" - ], - "Description": "CrossMap converts genome coordinates or annotation files between genome assemblies", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://crossmap.sourceforge.net/", - "ToolShed categories": [ - "Convert Formats", - "Genomic Interval Operations" - ], - "ToolShed id": "crossmap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap", - "Galaxy wrapper version": "0.6.1", - "Conda id": "crossmap", - "Conda version": "0.7.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cutadapt", - "Galaxy tool ids": [ - "cutadapt" - ], - "Description": "Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).", - "bio.tool id": "cutadapt", - "bio.tool ids": [ - "cutadapt" - ], - "biii": null, - "bio.tool name": "Cutadapt", - "bio.tool description": "Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.", - "EDAM operation": [ - "Sequence trimming", - "Primer removal", - "Read pre-processing" - ], - "EDAM topic": [ - "Genomics", - "Probes and primers", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://cutadapt.readthedocs.org/en/stable/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "cutadapt", - "Galaxy wrapper owner": "lparsons", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt", - "Galaxy wrapper version": "4.8", - "Conda id": "cutadapt", - "Conda version": "4.8", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "Primer removal", - "Read pre-processing" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Probes and primers", - "Sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cutesv", - "Galaxy tool ids": [ - "cutesv" - ], - "Description": "Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.", - "bio.tool id": "cuteSV", - "bio.tool ids": [ - "cuteSV" - ], - "biii": null, - "bio.tool name": "cuteSV", - "bio.tool description": "Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis", - "EDAM operation": [ - "Split read mapping", - "Genotyping", - "Structural variation detection" - ], - "EDAM topic": [ - "DNA structural variation", - "Sequencing", - "Computer science" - ], - "Status": "To update", - "Source": "https://github.com/tjiangHIT/cuteSV", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "cutesv", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv", - "Galaxy wrapper version": "1.0.8", - "Conda id": "cutesv", - "Conda version": "2.1.1", - "EDAM operation (no superclasses)": [ - "Split read mapping", - "Genotyping", - "Structural variation detection" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Computer science" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cwpair2", - "Galaxy tool ids": [ - "cwpair2" - ], - "Description": "Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "cwpair2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2", - "Galaxy wrapper version": "1.1.1", - "Conda id": "matplotlib", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dada2", - "Galaxy tool ids": [ - "dada2_assignTaxonomyAddspecies", - "dada2_dada", - "dada2_filterAndTrim", - "dada2_learnErrors", - "dada2_makeSequenceTable", - "dada2_mergePairs", - "dada2_plotComplexity", - "dada2_plotQualityProfile", - "dada2_removeBimeraDenovo", - "dada2_seqCounts" - ], - "Description": "DADA2 wrappers", - "bio.tool id": "dada2", - "bio.tool ids": [ - "dada2" - ], - "biii": null, - "bio.tool name": "dada2", - "bio.tool description": "This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.", - "EDAM operation": [ - "Variant calling", - "DNA barcoding" - ], - "EDAM topic": [ - "Sequencing", - "Genetic variation", - "Microbial ecology", - "Metagenomics" - ], - "Status": "To update", - "Source": "https://benjjneb.github.io/dada2/index.html", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "dada2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2", - "Galaxy wrapper version": null, - "Conda id": "bioconductor-dada2", - "Conda version": "1.30.0", - "EDAM operation (no superclasses)": [ - "Variant calling", - "DNA barcoding" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Genetic variation", - "Microbial ecology", - "Metagenomics" - ], - "Available on UseGalaxy.org": 10, - "Available on UseGalaxy.org.au": 10, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 10 - }, - { - "Galaxy wrapper id": "das_tool", - "Galaxy tool ids": [ - "Fasta_to_Contig2Bin", - "das_tool" - ], - "Description": "DAS Tool for genome resolved metagenomics", - "bio.tool id": "dastool", - "bio.tool ids": [ - "dastool" - ], - "biii": null, - "bio.tool name": "dastool", - "bio.tool description": "DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.", - "EDAM operation": [ - "Read binning" - ], - "EDAM topic": [ - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/cmks/DAS_Tool", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "das_tool", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool", - "Galaxy wrapper version": "1.1.7", - "Conda id": "das_tool", - "Conda version": "1.1.7", - "EDAM operation (no superclasses)": [ - "Read binning" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "data_source_iris_tcga", - "Galaxy tool ids": [ - "data_source_iris_tcga" - ], - "Description": "IRIS-TCGA Data source tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "data_source_iris_tcga", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga", - "Galaxy wrapper version": "1.0.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "datamash", - "Galaxy tool ids": [ - "datamash_ops", - "datamash_reverse", - "datamash_transpose" - ], - "Description": "GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.gnu.org/software/datamash/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash", - "Galaxy wrapper version": "1.8", - "Conda id": "datamash", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "decontaminator", - "Galaxy tool ids": [ - "decontaminator" - ], - "Description": "Deep Learning method for novel virus detection in sequencing data", - "bio.tool id": "decontaminator", - "bio.tool ids": [ - "decontaminator" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/cbib/decontaminator", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "decontaminator", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator", - "Galaxy wrapper version": "1.0.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "deepmicro", - "Galaxy tool ids": [ - "deepmicro" - ], - "Description": "Representation learning and classification framework", - "bio.tool id": "DeepMicro", - "bio.tool ids": [ - "DeepMicro" - ], - "biii": null, - "bio.tool name": "DeepMicro", - "bio.tool description": "Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.", - "EDAM operation": [ - "Essential dynamics", - "Splitting", - "Community profiling" - ], - "EDAM topic": [ - "Microbial ecology", - "Machine learning", - "Pathology", - "Public health and epidemiology", - "Allergy, clinical immunology and immunotherapeutics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/paulzierep/DeepMicro", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "deepmicro", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/paulzierep/DeepMicro", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro", - "Galaxy wrapper version": "1.4", - "Conda id": "deepmicro", - "Conda version": "1.4", - "EDAM operation (no superclasses)": [ - "Essential dynamics", - "Splitting" - ], - "EDAM topic (no superclasses)": [ - "Microbial ecology", - "Machine learning", - "Pathology", - "Public health and epidemiology", - "Allergy, clinical immunology and immunotherapeutics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "deepsig", - "Galaxy tool ids": [ - "deepsig" - ], - "Description": "Predictor of signal peptides in proteins based on deep learning", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/BolognaBiocomp/deepsig", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "deepsig", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig", - "Galaxy wrapper version": "1.2.5", - "Conda id": "deepsig", - "Conda version": "1.2.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "deepvariant", - "Galaxy tool ids": [ - "deepvariant" - ], - "Description": "DeepVariant is a deep learning-based variant caller", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/google/deepvariant", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "deepvariant", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant", - "Galaxy wrapper version": "1.5.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "deg_annotate", - "Galaxy tool ids": [ - "deg_annotate" - ], - "Description": "Annotate DESeq2/DEXSeq output tables", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "deg_annotate", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate", - "Galaxy wrapper version": "1.1.0", - "Conda id": "bedtools", - "Conda version": "2.31.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "delly", - "Galaxy tool ids": [ - "delly_call", - "delly_classify", - "delly_cnv", - "delly_filter", - "delly_lr", - "delly_merge" - ], - "Description": "Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.", - "bio.tool id": "delly2", - "bio.tool ids": [ - "delly2" - ], - "biii": null, - "bio.tool name": "Delly2", - "bio.tool description": "Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.", - "EDAM operation": [ - "Indel detection", - "Structural variation detection", - "Variant calling", - "Genotyping", - "Genetic variation analysis" - ], - "EDAM topic": [ - "DNA structural variation", - "Sequencing", - "Pathology", - "Genomics", - "Genetic variation", - "Bioinformatics", - "Population genomics", - "Rare diseases" - ], - "Status": "To update", - "Source": "https://github.com/dellytools/delly", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "delly", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly", - "Galaxy wrapper version": "0.9.1", - "Conda id": "delly", - "Conda version": "1.2.6", - "EDAM operation (no superclasses)": [ - "Indel detection", - "Structural variation detection", - "Genotyping" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Genetic variation", - "Bioinformatics", - "Population genomics", - "Rare diseases" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "deseq2", - "Galaxy tool ids": [ - "deseq2" - ], - "Description": "Differential gene expression analysis based on the negative binomial distribution", - "bio.tool id": "DESeq2", - "bio.tool ids": [ - "DESeq2" - ], - "biii": null, - "bio.tool name": "DESeq2", - "bio.tool description": "R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.", - "EDAM operation": [ - "Differential gene expression analysis", - "RNA-Seq analysis" - ], - "EDAM topic": [ - "RNA-Seq" - ], - "Status": "To update", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "deseq2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2", - "Galaxy wrapper version": "2.11.40.8", - "Conda id": "bioconductor-deseq2", - "Conda version": "1.42.0", - "EDAM operation (no superclasses)": [ - "Differential gene expression analysis", - "RNA-Seq analysis" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "dexseq", - "Galaxy tool ids": [ - "dexseq", - "dexseq_count", - "plotdexseq" - ], - "Description": "Inference of differential exon usage in RNA-Seq", - "bio.tool id": "dexseq", - "bio.tool ids": [ - "dexseq" - ], - "biii": null, - "bio.tool name": "DEXSeq", - "bio.tool description": "The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.", - "EDAM operation": [ - "Enrichment analysis", - "Exonic splicing enhancer prediction" - ], - "EDAM topic": [ - "RNA-Seq" - ], - "Status": "Up-to-date", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "dexseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq", - "Galaxy wrapper version": "1.48.0", - "Conda id": "bioconductor-dexseq", - "Conda version": "1.48.0", - "EDAM operation (no superclasses)": [ - "Enrichment analysis", - "Exonic splicing enhancer prediction" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "diamond", - "Galaxy tool ids": [ - "bg_diamond", - "bg_diamond_makedb", - "bg_diamond_view" - ], - "Description": "DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.", - "bio.tool id": "diamond", - "bio.tool ids": [ - "diamond" - ], - "biii": null, - "bio.tool name": "Diamond", - "bio.tool description": "Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.", - "EDAM operation": [ - "Sequence alignment analysis" - ], - "EDAM topic": [ - "Sequence analysis", - "Proteins" - ], - "Status": "To update", - "Source": "https://github.com/bbuchfink/diamond", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "diamond", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond", - "Galaxy wrapper version": "2.0.15", - "Conda id": "diamond", - "Conda version": "2.1.9", - "EDAM operation (no superclasses)": [ - "Sequence alignment analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Proteins" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "diffbind", - "Galaxy tool ids": [ - "diffbind" - ], - "Description": "Diffbind provides functions for processing ChIP-Seq data.", - "bio.tool id": "diffbind", - "bio.tool ids": [ - "diffbind" - ], - "biii": null, - "bio.tool name": "DiffBind", - "bio.tool description": "Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.", - "EDAM operation": [ - "Differential binding analysis" - ], - "EDAM topic": [ - "ChIP-seq" - ], - "Status": "To update", - "Source": "http://bioconductor.org/packages/release/bioc/html/DiffBind.html", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "diffbind", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind", - "Galaxy wrapper version": "2.10.0", - "Conda id": "bioconductor-diffbind", - "Conda version": "3.12.0", - "EDAM operation (no superclasses)": [ - "Differential binding analysis" - ], - "EDAM topic (no superclasses)": [ - "ChIP-seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "dimet", - "Galaxy tool ids": [ - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@", - "dimet_@EXECUTABLE@" - ], - "Description": "DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/cbib/DIMet", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet", - "Galaxy wrapper version": "0.2.4", - "Conda id": "dimet", - "Conda version": "0.2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "disco", - "Galaxy tool ids": [ - "disco" - ], - "Description": "DISCO is a overlap-layout-consensus (OLC) metagenome assembler", - "bio.tool id": "disco", - "bio.tool ids": [ - "disco" - ], - "biii": null, - "bio.tool name": "DISCO", - "bio.tool description": "DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.", - "EDAM operation": [ - "Protein sequence analysis" - ], - "EDAM topic": [ - "Structure determination" - ], - "Status": "To update", - "Source": "http://disco.omicsbio.org/", - "ToolShed categories": [ - "Metagenomics", - "Assembly" - ], - "ToolShed id": "disco", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco", - "Galaxy wrapper version": null, - "Conda id": "disco", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [ - "Protein sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Structure determination" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dnabot", - "Galaxy tool ids": [ - "dnabot" - ], - "Description": "DNA assembly using BASIC on OpenTrons", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "dnabot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot", - "Galaxy wrapper version": "3.1.0", - "Conda id": "dnabot", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dnaweaver", - "Galaxy tool ids": [ - "dnaweaver" - ], - "Description": "Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/Edinburgh-Genome-Foundry/DnaWeaver", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "dnaweaver", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver", - "Galaxy wrapper version": "1.0.2", - "Conda id": "dnaweaver_synbiocad", - "Conda version": "1.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dram", - "Galaxy tool ids": [ - "dram_annotate", - "dram_distill", - "dram_merge_annotations", - "dram_neighborhoods", - "dram_strainer" - ], - "Description": "DRAM for distilling microbial metabolism to automate the curation of microbiome function", - "bio.tool id": "dram", - "bio.tool ids": [ - "dram" - ], - "biii": null, - "bio.tool name": "DRAM", - "bio.tool description": "Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes", - "EDAM operation": [ - "Gene functional annotation" - ], - "EDAM topic": [ - "Metagenomics", - "Biological databases", - "Molecular genetics" - ], - "Status": "To update", - "Source": "https://github.com/WrightonLabCSU/DRAM", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "dram", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram", - "Galaxy wrapper version": "1.3.5", - "Conda id": "dram", - "Conda version": "1.5.0", - "EDAM operation (no superclasses)": [ - "Gene functional annotation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Biological databases", - "Molecular genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "drep", - "Galaxy tool ids": [ - "drep_compare", - "drep_dereplicate" - ], - "Description": "dRep compares and dereplicates genome sets", - "bio.tool id": "drep", - "bio.tool ids": [ - "drep" - ], - "biii": null, - "bio.tool name": "dRep", - "bio.tool description": "Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.", - "EDAM operation": [ - "Genome comparison" - ], - "EDAM topic": [ - "Metagenomics", - "Genomics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/MrOlm/drep", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "drep", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep", - "Galaxy wrapper version": "3.5.0", - "Conda id": "drep", - "Conda version": "3.5.0", - "EDAM operation (no superclasses)": [ - "Genome comparison" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "dropletutils", - "Galaxy tool ids": [ - "dropletutils" - ], - "Description": "DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data", - "bio.tool id": "dropletutils", - "bio.tool ids": [ - "dropletutils" - ], - "biii": null, - "bio.tool name": "DropletUtils", - "bio.tool description": "Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.", - "EDAM operation": [ - "Loading", - "Community profiling" - ], - "EDAM topic": [ - "Gene expression", - "RNA-seq", - "Sequencing", - "Transcriptomics" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "dropletutils", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils", - "Galaxy wrapper version": "1.10.0", - "Conda id": "bioconductor-dropletutils", - "Conda version": "1.22.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Transcriptomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ebi_tools", - "Galaxy tool ids": [ - "ebi_metagenomics_run_downloader", - "ebi_search_rest_results" - ], - "Description": "Tools to query and download data from several EMBL-EBI databases", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.ebi.ac.uk/services/all", - "ToolShed categories": [ - "Web Services", - "Data Source" - ], - "ToolShed id": "ebi_tools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools", - "Galaxy wrapper version": "0.1.0", - "Conda id": "six", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "edger", - "Galaxy tool ids": [ - "edger" - ], - "Description": "Perform RNA-Seq differential expression analysis using edgeR pipeline", - "bio.tool id": "edger", - "bio.tool ids": [ - "edger" - ], - "biii": null, - "bio.tool name": "edgeR", - "bio.tool description": "Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.", - "EDAM operation": [ - "Differential gene expression analysis" - ], - "EDAM topic": [ - "Genetics", - "RNA-Seq", - "ChIP-seq" - ], - "Status": "To update", - "Source": "http://bioconductor.org/packages/release/bioc/html/edgeR.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "edger", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger", - "Galaxy wrapper version": "3.36.0", - "Conda id": "bioconductor-edger", - "Conda version": "4.0.16", - "EDAM operation (no superclasses)": [ - "Differential gene expression analysis" - ], - "EDAM topic (no superclasses)": [ - "Genetics", - "RNA-Seq", - "ChIP-seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "egsea", - "Galaxy tool ids": [ - "egsea" - ], - "Description": "This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing", - "bio.tool id": "egsea", - "bio.tool ids": [ - "egsea" - ], - "biii": null, - "bio.tool name": "EGSEA", - "bio.tool description": "This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.", - "EDAM operation": [ - "Gene set testing" - ], - "EDAM topic": [ - "Systems biology" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/EGSEA.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "egsea", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea", - "Galaxy wrapper version": "1.20.0", - "Conda id": "bioconductor-egsea", - "Conda version": "1.28.0", - "EDAM operation (no superclasses)": [ - "Gene set testing" - ], - "EDAM topic (no superclasses)": [ - "Systems biology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "emboss_5", - "Galaxy tool ids": [ - "EMBOSS: antigenic1", - "EMBOSS: backtranseq2", - "EMBOSS: banana3", - "EMBOSS: biosed4", - "EMBOSS: btwisted5", - "EMBOSS: cai6", - "EMBOSS: cai_custom6", - "EMBOSS: chaos7", - "EMBOSS: charge8", - "EMBOSS: checktrans9", - "EMBOSS: chips10", - "EMBOSS: cirdna11", - "EMBOSS: codcmp12", - "EMBOSS: coderet13", - "EMBOSS: compseq14", - "EMBOSS: cpgplot15", - "EMBOSS: cpgreport16", - "EMBOSS: cusp17", - "EMBOSS: cutseq18", - "EMBOSS: dan19", - "EMBOSS: degapseq20", - "EMBOSS: descseq21", - "EMBOSS: diffseq22", - "EMBOSS: digest23", - "EMBOSS: dotmatcher24", - "EMBOSS: dotpath25", - "EMBOSS: dottup26", - "EMBOSS: dreg27", - "EMBOSS: einverted28", - "EMBOSS: epestfind29", - "EMBOSS: equicktandem31", - "EMBOSS: est2genome32", - "EMBOSS: etandem33", - "EMBOSS: extractfeat34", - "EMBOSS: extractseq35", - "EMBOSS: freak36", - "EMBOSS: fuzznuc37", - "EMBOSS: fuzzpro38", - "EMBOSS: fuzztran39", - "EMBOSS: garnier40", - "EMBOSS: geecee41", - "EMBOSS: getorf42", - "EMBOSS: helixturnhelix43", - "EMBOSS: hmoment44", - "EMBOSS: iep45", - "EMBOSS: infoseq46", - "EMBOSS: isochore47", - "EMBOSS: lindna48", - "EMBOSS: marscan49", - "EMBOSS: maskfeat50", - "EMBOSS: maskseq51", - "EMBOSS: matcher52", - "EMBOSS: megamerger53", - "EMBOSS: merger54", - "EMBOSS: msbar55", - "EMBOSS: needle56", - "EMBOSS: newcpgreport57", - "EMBOSS: newcpgseek58", - "EMBOSS: newseq59", - "EMBOSS: noreturn60", - "EMBOSS: notseq61", - "EMBOSS: nthseq62", - "EMBOSS: octanol63", - "EMBOSS: oddcomp64", - "EMBOSS: palindrome65", - "EMBOSS: pasteseq66", - "EMBOSS: patmatdb67", - "EMBOSS: pepcoil68", - "EMBOSS: pepinfo69", - "EMBOSS: pepnet70", - "EMBOSS: pepstats71", - "EMBOSS: pepwheel72", - "EMBOSS: pepwindow73", - "EMBOSS: pepwindowall74", - "EMBOSS: plotcon75", - "EMBOSS: plotorf76", - "EMBOSS: polydot77", - "EMBOSS: preg78", - "EMBOSS: prettyplot79", - "EMBOSS: prettyseq80", - "EMBOSS: primersearch81", - "EMBOSS: revseq82", - "EMBOSS: seqmatchall83", - "EMBOSS: seqret84", - "EMBOSS: showfeat85", - "EMBOSS: shuffleseq87", - "EMBOSS: sigcleave88", - "EMBOSS: sirna89", - "EMBOSS: sixpack90", - "EMBOSS: skipseq91", - "EMBOSS: splitter92", - "EMBOSS: supermatcher95", - "EMBOSS: syco96", - "EMBOSS: tcode97", - "EMBOSS: textsearch98", - "EMBOSS: tmap99", - "EMBOSS: tranalign100", - "EMBOSS: transeq101", - "EMBOSS: trimest102", - "EMBOSS: trimseq103", - "EMBOSS: twofeat104", - "EMBOSS: union105", - "EMBOSS: vectorstrip106", - "EMBOSS: water107", - "EMBOSS: wobble108", - "EMBOSS: wordcount109", - "EMBOSS: wordmatch110" - ], - "Description": "Galaxy wrappers for EMBOSS version 5.0.0 tools", - "bio.tool id": "emboss", - "bio.tool ids": [ - "emboss" - ], - "biii": null, - "bio.tool name": "EMBOSS", - "bio.tool description": "Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.", - "EDAM operation": [ - "Sequence analysis", - "Local alignment", - "Sequence alignment analysis", - "Global alignment", - "Sequence alignment" - ], - "EDAM topic": [ - "Molecular biology", - "Sequence analysis", - "Biology" - ], - "Status": "To update", - "Source": "http://emboss.open-bio.org/", - "ToolShed categories": [ - "Sequence Analysis", - "Fasta Manipulation" - ], - "ToolShed id": "emboss_5", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5", - "Galaxy wrapper version": "5.0.0", - "Conda id": "emboss", - "Conda version": "6.6.0", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Local alignment", - "Sequence alignment analysis", - "Global alignment", - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Molecular biology", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 107, - "Available on UseGalaxy.org.au": 107, - "Available on UseGalaxy.eu": 107, - "Available on UseGalaxy.org.fr": 107 - }, - { - "Galaxy wrapper id": "ena_upload", - "Galaxy tool ids": [ - "ena_upload" - ], - "Description": "Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). ", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/usegalaxy-eu/ena-upload-cli", - "ToolShed categories": [ - "Data Export" - ], - "ToolShed id": "ena_upload", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload", - "Galaxy wrapper version": "0.7.1", - "Conda id": "ena-upload-cli", - "Conda version": "0.7.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "enasearch", - "Galaxy tool ids": [ - "enasearch_retrieve_analysis_report", - "enasearch_retrieve_data", - "enasearch_retrieve_run_report", - "enasearch_retrieve_taxons", - "enasearch_search_data" - ], - "Description": "A Python library for interacting with ENA's API", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/bebatut/enasearch", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "enasearch", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch", - "Galaxy wrapper version": null, - "Conda id": "enasearch", - "Conda version": "0.2.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ensembl_vep", - "Galaxy tool ids": [ - "ensembl_vep" - ], - "Description": "Ensembl VEP: Annotate VCFs with variant effect predictions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Ensembl/ensembl-vep", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "ensembl_vep", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep", - "Galaxy wrapper version": "110.1", - "Conda id": "ensembl-vep", - "Conda version": "112.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "episcanpy", - "Galaxy tool ids": [ - "episcanpy_build_matrix", - "episcanpy_cluster_embed", - "episcanpy_preprocess" - ], - "Description": "EpiScanpy – Epigenomics single cell analysis in python", - "bio.tool id": "episcanpy", - "bio.tool ids": [ - "episcanpy" - ], - "biii": null, - "bio.tool name": "epiScanpy", - "bio.tool description": "Epigenomics Single Cell Analysis in Python.", - "EDAM operation": [ - "Enrichment analysis", - "Imputation" - ], - "EDAM topic": [ - "Epigenomics", - "Cell biology", - "DNA" - ], - "Status": "To update", - "Source": "https://github.com/colomemaria/epiScanpy", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "episcanpy", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy", - "Galaxy wrapper version": "0.3.2", - "Conda id": "episcanpy", - "Conda version": "0.4.0", - "EDAM operation (no superclasses)": [ - "Enrichment analysis", - "Imputation" - ], - "EDAM topic (no superclasses)": [ - "Epigenomics", - "Cell biology", - "DNA" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "exomedepth", - "Galaxy tool ids": [ - "exomedepth" - ], - "Description": "ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data", - "bio.tool id": "exomedepth", - "bio.tool ids": [ - "exomedepth" - ], - "biii": null, - "bio.tool name": "ExomeDepth", - "bio.tool description": "Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.", - "EDAM operation": [ - "Sequence analysis", - "Variant calling", - "Genotyping", - "Copy number estimation" - ], - "EDAM topic": [ - "Exome sequencing", - "Gene transcripts", - "Mapping", - "Sequencing", - "Genetic variation", - "Rare diseases" - ], - "Status": "To update", - "Source": "https://cran.r-project.org/package=ExomeDepth", - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": "exomedepth", - "Galaxy wrapper owner": "crs4", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth", - "Galaxy wrapper version": "1.1.0", - "Conda id": "r-exomedepth", - "Conda version": "1.1.16", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Variant calling", - "Genotyping", - "Copy number estimation" - ], - "EDAM topic (no superclasses)": [ - "Exome sequencing", - "Gene transcripts", - "Mapping", - "Genetic variation", - "Rare diseases" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "exonerate", - "Galaxy tool ids": [ - "exonerate" - ], - "Description": "Exonerate is a generic tool for pairwise sequence comparison.", - "bio.tool id": "exonerate", - "bio.tool ids": [ - "exonerate" - ], - "biii": null, - "bio.tool name": "Exonerate", - "bio.tool description": "A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.", - "EDAM operation": [ - "Pairwise sequence alignment", - "Protein threading", - "Genome alignment" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequence sites, features and motifs", - "Molecular interactions, pathways and networks" - ], - "Status": "Up-to-date", - "Source": "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "exonerate", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate", - "Galaxy wrapper version": "2.4.0", - "Conda id": "exonerate", - "Conda version": "2.4.0", - "EDAM operation (no superclasses)": [ - "Pairwise sequence alignment", - "Protein threading", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Sequence sites, features and motifs", - "Molecular interactions, pathways and networks" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "export2graphlan", - "Galaxy tool ids": [ - "export2graphlan" - ], - "Description": "export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn", - "bio.tool id": "export2graphlan", - "bio.tool ids": [ - "export2graphlan" - ], - "biii": null, - "bio.tool name": "export2graphlan", - "bio.tool description": "export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.", - "EDAM operation": [ - "Conversion" - ], - "EDAM topic": [ - "Taxonomy", - "Metabolomics", - "Biomarkers" - ], - "Status": "To update", - "Source": "https://bitbucket.org/CibioCM/export2graphlan/overview", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "export2graphlan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan", - "Galaxy wrapper version": "0.20", - "Conda id": "export2graphlan", - "Conda version": "0.22", - "EDAM operation (no superclasses)": [ - "Conversion" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy", - "Metabolomics", - "Biomarkers" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "extract_genomic_dna", - "Galaxy tool ids": [ - "Extract genomic DNA 1" - ], - "Description": "Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "extract_genomic_dna", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna", - "Galaxy wrapper version": "3.0.3+galaxy2", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "falco", - "Galaxy tool ids": [ - "falco" - ], - "Description": "A high throughput sequence QC analysis tool", - "bio.tool id": "falco", - "bio.tool ids": [ - "falco" - ], - "biii": null, - "bio.tool name": "Falco", - "bio.tool description": "A high-speed FastQC emulation for quality control of sequencing data.", - "EDAM operation": [ - "Sequencing quality control", - "Visualisation", - "Read mapping" - ], - "EDAM topic": [ - "Workflows", - "Mapping", - "Imaging" - ], - "Status": "To update", - "Source": "https://github.com/smithlabcode/falco/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "falco", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco", - "Galaxy wrapper version": "1.2.2+galaxy0", - "Conda id": "falco", - "Conda version": "1.2.2", - "EDAM operation (no superclasses)": [ - "Sequencing quality control", - "Visualisation", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Workflows", - "Mapping", - "Imaging" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fargene", - "Galaxy tool ids": [ - "fargene" - ], - "Description": "fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )", - "bio.tool id": "fargene", - "bio.tool ids": [ - "fargene" - ], - "biii": null, - "bio.tool name": "fARGene", - "bio.tool description": "fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.", - "EDAM operation": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic": [ - "Metagenomics", - "Microbiology", - "Public health and epidemiology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/fannyhb/fargene", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fargene", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene", - "Galaxy wrapper version": "0.1", - "Conda id": "fargene", - "Conda version": "0.1", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbiology", - "Public health and epidemiology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_nucleotide_color_plot", - "Galaxy tool ids": [ - "fasta_nucleotide_color_plot" - ], - "Description": "Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "fasta_nucleotide_color_plot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot", - "Galaxy wrapper version": "1.0.1", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_stats", - "Galaxy tool ids": [ - "fasta-stats" - ], - "Description": "Display summary statistics for a fasta file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fasta_stats", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats", - "Galaxy wrapper version": "2.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastani", - "Galaxy tool ids": [ - "fastani" - ], - "Description": "Fast alignment-free computation of whole-genome Average Nucleotide Identity", - "bio.tool id": "fastani", - "bio.tool ids": [ - "fastani" - ], - "biii": null, - "bio.tool name": "FastANI", - "bio.tool description": "FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.", - "EDAM operation": [ - "Genome alignment", - "Sequence similarity search" - ], - "EDAM topic": [ - "Microbiology", - "Genetic variation" - ], - "Status": "To update", - "Source": "https://github.com/ParBLiSS/FastANI", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fastani", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani", - "Galaxy wrapper version": "1.3", - "Conda id": "fastani", - "Conda version": "1.34", - "EDAM operation (no superclasses)": [ - "Genome alignment", - "Sequence similarity search" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastk", - "Galaxy tool ids": [ - "fastk_fastk" - ], - "Description": "FastK: A K-mer counter (for HQ assembly data sets)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/thegenemyers/FASTK", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "fastk", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk", - "Galaxy wrapper version": "1.0.0", - "Conda id": "fastk", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastp", - "Galaxy tool ids": [ - "fastp" - ], - "Description": "Fast all-in-one preprocessing for FASTQ files", - "bio.tool id": "fastp", - "bio.tool ids": [ - "fastp" - ], - "biii": null, - "bio.tool name": "fastp", - "bio.tool description": "A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.", - "EDAM operation": [ - "Sequencing quality control", - "Sequence contamination filtering" - ], - "EDAM topic": [ - "Sequence analysis", - "Probes and primers" - ], - "Status": "Up-to-date", - "Source": "https://github.com/OpenGene/fastp", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fastp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp", - "Galaxy wrapper version": "0.23.4", - "Conda id": "fastp", - "Conda version": "0.23.4", - "EDAM operation (no superclasses)": [ - "Sequence contamination filtering" - ], - "EDAM topic (no superclasses)": [ - "Probes and primers" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastqc", - "Galaxy tool ids": [ - "fastqc" - ], - "Description": "Read QC reports using FastQC", - "bio.tool id": "fastqc", - "bio.tool ids": [ - "fastqc" - ], - "biii": null, - "bio.tool name": "FastQC", - "bio.tool description": "This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.", - "EDAM operation": [ - "Sequence composition calculation", - "Sequencing quality control", - "Statistical calculation" - ], - "EDAM topic": [ - "Sequencing", - "Data quality management", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastqc", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc", - "Galaxy wrapper version": "0.74+galaxy0", - "Conda id": "fastqc", - "Conda version": "0.12.1", - "EDAM operation (no superclasses)": [ - "Sequence composition calculation", - "Sequencing quality control", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Data quality management", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastqe", - "Galaxy tool ids": [ - "fastqe" - ], - "Description": "FASTQE", - "bio.tool id": "fastqe", - "bio.tool ids": [ - "fastqe" - ], - "biii": null, - "bio.tool name": "FASTQE", - "bio.tool description": "Compute quality stats for FASTQ files and print those stats as emoji... for some reason.", - "EDAM operation": [ - "Sequencing quality control" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequencing" - ], - "Status": "To update", - "Source": "https://fastqe.com/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fastqe", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe", - "Galaxy wrapper version": "0.3.1+galaxy0", - "Conda id": "fastqe", - "Conda version": "0.3.1", - "EDAM operation (no superclasses)": [ - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fasttree", - "Galaxy tool ids": [ - "fasttree" - ], - "Description": "FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL", - "bio.tool id": "fasttree", - "bio.tool ids": [ - "fasttree" - ], - "biii": null, - "bio.tool name": "FastTree", - "bio.tool description": "Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.", - "EDAM operation": [ - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)" - ], - "EDAM topic": [ - "Phylogenetics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.microbesonline.org/fasttree/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "fasttree", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree", - "Galaxy wrapper version": "2.1.10", - "Conda id": "fasttree", - "Conda version": "2.1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "featurecounts", - "Galaxy tool ids": [ - "featurecounts" - ], - "Description": "featureCounts counts the number of reads aligned to defined masked regions in a reference genome", - "bio.tool id": "featurecounts", - "bio.tool ids": [ - "featurecounts" - ], - "biii": null, - "bio.tool name": "FeatureCounts", - "bio.tool description": "featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.", - "EDAM operation": [ - "Read summarisation", - "RNA-Seq quantification" - ], - "EDAM topic": [ - "RNA-Seq" - ], - "Status": "To update", - "Source": "http://bioinf.wehi.edu.au/featureCounts", - "ToolShed categories": [ - "RNA", - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "featurecounts", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts", - "Galaxy wrapper version": "2.0.3", - "Conda id": "subread", - "Conda version": "2.0.6", - "EDAM operation (no superclasses)": [ - "Read summarisation", - "RNA-Seq quantification" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "feelnc", - "Galaxy tool ids": [ - "feelnc" - ], - "Description": "Galaxy wrapper for FEELnc", - "bio.tool id": "feelnc", - "bio.tool ids": [ - "feelnc" - ], - "biii": null, - "bio.tool name": "FEELnc", - "bio.tool description": "A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.", - "EDAM operation": [ - "Annotation", - "Classification" - ], - "EDAM topic": [ - "RNA-seq", - "Functional, regulatory and non-coding RNA" - ], - "Status": "To update", - "Source": "https://github.com/tderrien/FEELnc", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "feelnc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc", - "Galaxy wrapper version": "0.2.1", - "Conda id": "feelnc", - "Conda version": "0.2", - "EDAM operation (no superclasses)": [ - "Annotation", - "Classification" - ], - "EDAM topic (no superclasses)": [ - "Functional, regulatory and non-coding RNA" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fermikit", - "Galaxy tool ids": [ - "fermi2", - "fermikit_variants" - ], - "Description": "FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/lh3/fermikit", - "ToolShed categories": [ - "Assembly", - "Variant Analysis" - ], - "ToolShed id": "fermikit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit", - "Galaxy wrapper version": "r193", - "Conda id": "fermi2", - "Conda version": "r193", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fgsea", - "Galaxy tool ids": [ - "fgsea" - ], - "Description": "Perform gene set testing using fgsea", - "bio.tool id": "fgsea", - "bio.tool ids": [ - "fgsea" - ], - "biii": null, - "bio.tool name": "fgsea", - "bio.tool description": "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.", - "EDAM operation": [ - "Gene-set enrichment analysis" - ], - "EDAM topic": [ - "Genetics" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/fgsea.html", - "ToolShed categories": [ - "Visualization", - "Transcriptomics", - "Statistics" - ], - "ToolShed id": "fgsea", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea", - "Galaxy wrapper version": "1.8.0+galaxy1", - "Conda id": "bioconductor-fgsea", - "Conda version": "1.28.0", - "EDAM operation (no superclasses)": [ - "Gene-set enrichment analysis" - ], - "EDAM topic (no superclasses)": [ - "Genetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "filtlong", - "Galaxy tool ids": [ - "filtlong" - ], - "Description": "Filtlong - Filtering long reads by quality", - "bio.tool id": "filtlong", - "bio.tool ids": [ - "filtlong" - ], - "biii": null, - "bio.tool name": "Filtlong", - "bio.tool description": "Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.", - "EDAM operation": [ - "Filtering", - "Sequencing quality control" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/rrwick/Filtlong", - "ToolShed categories": [ - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "filtlong", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong", - "Galaxy wrapper version": "0.2.1", - "Conda id": "filtlong", - "Conda version": "0.2.1", - "EDAM operation (no superclasses)": [ - "Filtering", - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "flair", - "Galaxy tool ids": [ - "flair_collapse", - "flair_correct" - ], - "Description": "FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/BrooksLabUCSC/flair", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "flair", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair", - "Galaxy wrapper version": "1.5", - "Conda id": "flair", - "Conda version": "2.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "flash", - "Galaxy tool ids": [ - "flash" - ], - "Description": "Fast Length Adjustment of SHort reads", - "bio.tool id": "flash", - "bio.tool ids": [ - "flash" - ], - "biii": null, - "bio.tool name": "FLASH", - "bio.tool description": "Identifies paired-end reads which overlap in the middle, converting them to single long reads", - "EDAM operation": [ - "Read pre-processing", - "Sequence merging", - "Sequence assembly" - ], - "EDAM topic": [ - "Sequencing", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://ccb.jhu.edu/software/FLASH/", - "ToolShed categories": [ - "Assembly", - "Fastq Manipulation" - ], - "ToolShed id": "flash", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash", - "Galaxy wrapper version": "1.2.11", - "Conda id": "flash", - "Conda version": "1.2.11", - "EDAM operation (no superclasses)": [ - "Read pre-processing", - "Sequence merging", - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fraggenescan", - "Galaxy tool ids": [ - "fraggenescan" - ], - "Description": "Tool for finding (fragmented) genes in short read", - "bio.tool id": "fraggenescan", - "bio.tool ids": [ - "fraggenescan" - ], - "biii": null, - "bio.tool name": "FragGeneScan", - "bio.tool description": "Application for finding (fragmented) genes in short reads", - "EDAM operation": [ - "Gene prediction" - ], - "EDAM topic": [ - "Genetics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://sourceforge.net/projects/fraggenescan/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "fraggenescan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan", - "Galaxy wrapper version": null, - "Conda id": "fraggenescan", - "Conda version": "1.31", - "EDAM operation (no superclasses)": [ - "Gene prediction" - ], - "EDAM topic (no superclasses)": [ - "Genetics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "freebayes", - "Galaxy tool ids": [ - "freebayes", - "bamleftalign" - ], - "Description": "Galaxy Freebayes Bayesian genetic variant detector tool", - "bio.tool id": "freebayes", - "bio.tool ids": [ - "freebayes" - ], - "biii": null, - "bio.tool name": "FreeBayes", - "bio.tool description": "Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.", - "EDAM operation": [ - "Variant calling", - "Statistical calculation" - ], - "EDAM topic": [ - "Genomics", - "Genetic variation", - "Rare diseases" - ], - "Status": "To update", - "Source": "https://github.com/ekg/freebayes", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "freebayes", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes", - "Galaxy wrapper version": "1.3.6", - "Conda id": "freebayes", - "Conda version": "1.3.7", - "EDAM operation (no superclasses)": [ - "Variant calling", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Genetic variation", - "Rare diseases" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "freec", - "Galaxy tool ids": [ - "control_freec" - ], - "Description": "Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.", - "bio.tool id": "freec", - "bio.tool ids": [ - "freec" - ], - "biii": null, - "bio.tool name": "FREEC", - "bio.tool description": "A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.", - "EDAM operation": [ - "Copy number estimation", - "Variant calling", - "Genome alignment" - ], - "EDAM topic": [ - "DNA structural variation", - "Oncology", - "Human genetics", - "Data mining" - ], - "Status": "To update", - "Source": "http://boevalab.inf.ethz.ch/FREEC/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "control_freec", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec", - "Galaxy wrapper version": "11.6", - "Conda id": "gawk", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Copy number estimation", - "Variant calling", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Oncology", - "Human genetics", - "Data mining" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "freyja", - "Galaxy tool ids": [ - "freyja_aggregate_plot", - "freyja_boot", - "freyja_demix", - "freyja_variants" - ], - "Description": "lineage abundances estimation", - "bio.tool id": "freyja", - "bio.tool ids": [ - "freyja" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/andersen-lab/Freyja", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": "freyja", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja", - "Galaxy wrapper version": "1.4.4", - "Conda id": "freyja", - "Conda version": "1.5.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fsd", - "Galaxy tool ids": [ - "fsd", - "fsd_beforevsafter", - "fsd_regions", - "td" - ], - "Description": "Tool that plots a histogram of sizes of read families", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics" - ], - "ToolShed id": "duplex_family_size_distribution", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd", - "Galaxy wrapper version": "1.0.2", - "Conda id": "matplotlib", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "funannotate", - "Galaxy tool ids": [ - "funannotate_annotate", - "funannotate_clean", - "funannotate_compare", - "funannotate_predict", - "funannotate_sort" - ], - "Description": "Funannotate is a genome prediction, annotation, and comparison software package.", - "bio.tool id": "funannotate", - "bio.tool ids": [ - "funannotate" - ], - "biii": null, - "bio.tool name": "funannotate", - "bio.tool description": "funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "To update", - "Source": "https://funannotate.readthedocs.io", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate", - "Galaxy wrapper version": "1.8.15", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "gatk4", - "Galaxy tool ids": [ - "gatk4_mutect2" - ], - "Description": "A Galaxy wrapper for Mutect2 from GATK", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://software.broadinstitute.org/gatk/gatk4", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "gatk4_mutect2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4", - "Galaxy wrapper version": "4.1.7.0", - "Conda id": "gatk4", - "Conda version": "4.5.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gdcwebapp", - "Galaxy tool ids": [ - "data_source_gdcwebapp" - ], - "Description": "GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://bioinf.iasi.cnr.it/gdcwebapp/", - "ToolShed categories": [ - "Data Source", - "Convert Formats" - ], - "ToolShed id": "gdcwebapp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/fabio-cumbo/GDCWebApp4Galaxy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp", - "Galaxy wrapper version": "1.0.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gecko", - "Galaxy tool ids": [ - "gecko" - ], - "Description": "Ungapped genome comparison", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/otorreno/gecko", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gecko", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko", - "Galaxy wrapper version": "1.2", - "Conda id": "gecko", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gemini", - "Galaxy tool ids": [ - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_db_info", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_inheritance", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@", - "gemini_@BINARY@" - ], - "Description": "GEMINI: a flexible framework for exploring genome variation", - "bio.tool id": "gemini", - "bio.tool ids": [ - "gemini" - ], - "biii": null, - "bio.tool name": "GEMINI", - "bio.tool description": "GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.", - "EDAM operation": [ - "Sequence analysis", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/arq5x/gemini", - "ToolShed categories": [ - "Sequence Analysis", - "Next Gen Mappers" - ], - "ToolShed id": "gemini", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini", - "Galaxy wrapper version": "0.20.1", - "Conda id": "gemini", - "Conda version": "0.30.2", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "genebed_maf_to_fasta", - "Galaxy tool ids": [ - "GeneBed_Maf_Fasta2" - ], - "Description": "Stitch gene blocks given a set of coding exon intervals", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "genebed_maf_to_fasta", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta", - "Galaxy wrapper version": "1.0.1+galaxy0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "genehunter_modscore", - "Galaxy tool ids": [ - "genehunter_modscore" - ], - "Description": "Maximised LOD score pedigree analysis utility", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "genehunter_modscore", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore", - "Galaxy wrapper version": "3.0.0", - "Conda id": "ghm", - "Conda version": "3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "geneiobio", - "Galaxy tool ids": [ - "gene_iobio_display_generation_iframe" - ], - "Description": "Gene.iobio is an interactive tool for variant and trio analysis.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/iobio/gene.iobio", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "geneiobio", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio", - "Galaxy wrapper version": "4.7.1+galaxy1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "genetrack", - "Galaxy tool ids": [ - "genetrack" - ], - "Description": "Contains a tool that separately identifies peaks on the forward \"+” (W) and reverse “-” (C) strand.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "genetrack", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack", - "Galaxy wrapper version": null, - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "genomescope", - "Galaxy tool ids": [ - "genomescope" - ], - "Description": "Analyze unassembled short reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/tbenavi1/genomescope2.0", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "genomescope", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope", - "Galaxy wrapper version": "2.0", - "Conda id": "genomescope2", - "Conda version": "2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "genomic_super_signature", - "Galaxy tool ids": [ - "genomic_super_signature" - ], - "Description": "Interpretation of RNAseq experiments through robust, efficient comparison to public databases", - "bio.tool id": "genomicsupersignature", - "bio.tool ids": [ - "genomicsupersignature" - ], - "biii": null, - "bio.tool name": "GenomicSuperSignature", - "bio.tool description": "GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.", - "EDAM operation": [ - "Gene-set enrichment analysis", - "Essential dynamics", - "Deposition", - "Principal component visualisation", - "Dimensionality reduction" - ], - "EDAM topic": [ - "RNA-Seq", - "Transcriptomics", - "Microbial ecology", - "Genotype and phenotype", - "Microarray experiment" - ], - "Status": "To update", - "Source": "https://github.com/shbrief/GenomicSuperSignature", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "Transcriptomics" - ], - "ToolShed id": "genomic_super_signature", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature", - "Galaxy wrapper version": "1.2.0", - "Conda id": "bioconductor-genomicsupersignature", - "Conda version": "1.10.0", - "EDAM operation (no superclasses)": [ - "Gene-set enrichment analysis", - "Essential dynamics", - "Deposition", - "Principal component visualisation", - "Dimensionality reduction" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Transcriptomics", - "Microbial ecology", - "Genotype and phenotype", - "Microarray experiment" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "genrich", - "Galaxy tool ids": [ - "genrich" - ], - "Description": "Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/jsh58/Genrich", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "genrich", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/jsh58/Genrich", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich", - "Galaxy wrapper version": "0.5+galaxy2", - "Conda id": "genrich", - "Conda version": "0.6.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "get_hrun", - "Galaxy tool ids": [ - "get_hrun" - ], - "Description": "Annotate indel variants with homopolymer context", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "get_hrun", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun", - "Galaxy wrapper version": "0.5.9.2", - "Conda id": "pyfaidx", - "Conda version": "0.8.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "getorganelle", - "Galaxy tool ids": [ - "get_annotated_regions_from_gb", - "get_organelle_from_reads" - ], - "Description": "GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.", - "bio.tool id": "getorganelle", - "bio.tool ids": [ - "getorganelle" - ], - "biii": null, - "bio.tool name": "GetOrganelle", - "bio.tool description": "A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.", - "EDAM operation": [ - "De-novo assembly", - "Genome assembly", - "Mapping assembly", - "Mapping", - "Sequence trimming" - ], - "EDAM topic": [ - "Cell biology", - "Sequence assembly", - "Whole genome sequencing", - "Plant biology", - "Model organisms" - ], - "Status": "Up-to-date", - "Source": "https://github.com/Kinggerm/GetOrganelle", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "getorganelle", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle", - "Galaxy wrapper version": "1.7.7.1", - "Conda id": "getorganelle", - "Conda version": "1.7.7.1", - "EDAM operation (no superclasses)": [ - "De-novo assembly", - "Genome assembly", - "Mapping assembly", - "Mapping", - "Sequence trimming" - ], - "EDAM topic (no superclasses)": [ - "Cell biology", - "Sequence assembly", - "Whole genome sequencing", - "Plant biology", - "Model organisms" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gfa_to_fa", - "Galaxy tool ids": [ - "gfa_to_fa" - ], - "Description": "gfa_to_fa - Converting GFA format to Fasta format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://gfa-spec.github.io/GFA-spec/", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "gfa_to_fa", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa", - "Galaxy wrapper version": "0.1.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gff3_rebase", - "Galaxy tool ids": [ - "gff3.rebase" - ], - "Description": "Rebase a GFF against a parent GFF (e.g. an original genome)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gff3_rebase", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase", - "Galaxy wrapper version": "1.2", - "Conda id": "bcbiogff", - "Conda version": "0.6.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gffcompare", - "Galaxy tool ids": [ - "gffcompare" - ], - "Description": "Galaxy wrappers for Geo Pertea's GffCompare package.", - "bio.tool id": "gffcompare", - "bio.tool ids": [ - "gffcompare" - ], - "biii": null, - "bio.tool name": "gffcompare", - "bio.tool description": "Program for comparing, annotating, merging and tracking transcripts in GFF files.", - "EDAM operation": [ - "Sequence annotation" - ], - "EDAM topic": [ - "Nucleic acids", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/gpertea/gffcompare/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gffcompare", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare", - "Galaxy wrapper version": "0.12.6", - "Conda id": "gffcompare", - "Conda version": "0.12.6", - "EDAM operation (no superclasses)": [ - "Sequence annotation" - ], - "EDAM topic (no superclasses)": [ - "Nucleic acids", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gffread", - "Galaxy tool ids": [ - "gffread" - ], - "Description": "gffread filters and/or converts GFF3/GTF2 records", - "bio.tool id": "gffread", - "bio.tool ids": [ - "gffread" - ], - "biii": null, - "bio.tool name": "gffread", - "bio.tool description": "program for filtering, converting and manipulating GFF files", - "EDAM operation": [ - "Sequence annotation" - ], - "EDAM topic": [ - "Nucleic acids", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gffread", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread", - "Galaxy wrapper version": "0.12.7", - "Conda id": "gffread", - "Conda version": "0.12.7", - "EDAM operation (no superclasses)": [ - "Sequence annotation" - ], - "EDAM topic (no superclasses)": [ - "Nucleic acids", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ggplot2", - "Galaxy tool ids": [ - "ggplot2_heatmap", - "ggplot2_pca", - "ggplot2_histogram", - "ggplot2_point", - "ggplot2_violin" - ], - "Description": "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.", - "bio.tool id": "ggplot2", - "bio.tool ids": [ - "ggplot2" - ], - "biii": null, - "bio.tool name": "ggplot2", - "bio.tool description": "Plotting system for R, based on the grammar of graphics.", - "EDAM operation": [ - "Visualisation" - ], - "EDAM topic": [ - "Data visualisation" - ], - "Status": "To update", - "Source": "https://github.com/tidyverse/ggplot2", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2", - "Galaxy wrapper version": "3.4.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Data visualisation" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "ggupset", - "Galaxy tool ids": [ - "emc-ggupset" - ], - "Description": "Create Upset Plots with ggupset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/const-ae/ggupset", - "ToolShed categories": [ - "Graphics" - ], - "ToolShed id": "ggupset", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset", - "Galaxy wrapper version": "1.0", - "Conda id": "r-ggupset", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "glimmer", - "Galaxy tool ids": [ - "glimmer_acgt_content", - "glimmer_build_icm", - "glimmer_extract", - "glimmer_gbk_to_orf", - "glimmer_glimmer_to_gff", - "glimmer_long_orfs", - "glimmer_knowledge_based", - "glimmer_not_knowledge_based" - ], - "Description": "Glimmer makes gene predictions.", - "bio.tool id": "gemini", - "bio.tool ids": [ - "gemini" - ], - "biii": null, - "bio.tool name": "GEMINI", - "bio.tool description": "GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.", - "EDAM operation": [ - "Sequence analysis", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://ccb.jhu.edu/software/glimmer/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer", - "Galaxy wrapper version": null, - "Conda id": "glimmer", - "Conda version": "3.02", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "goenrichment", - "Galaxy tool ids": [ - "goenrichment", - "goslimmer" - ], - "Description": "Performs GO Enrichment analysis.", - "bio.tool id": "goenrichment", - "bio.tool ids": [ - "goenrichment" - ], - "biii": null, - "bio.tool name": "GOEnrichment", - "bio.tool description": "GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.", - "EDAM operation": [ - "Gene-set enrichment analysis" - ], - "EDAM topic": [ - "Transcriptomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/DanFaria/GOEnrichment", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment", - "Galaxy wrapper version": "2.0.1", - "Conda id": "goenrichment", - "Conda version": "2.0.1", - "EDAM operation (no superclasses)": [ - "Gene-set enrichment analysis" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "goseq", - "Galaxy tool ids": [ - "goseq" - ], - "Description": "goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data", - "bio.tool id": "goseq", - "bio.tool ids": [ - "goseq" - ], - "biii": null, - "bio.tool name": "GOseq", - "bio.tool description": "Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.", - "EDAM operation": [ - "Gene functional annotation" - ], - "EDAM topic": [ - "RNA-Seq" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/goseq.html", - "ToolShed categories": [ - "Statistics", - "RNA", - "Micro-array Analysis" - ], - "ToolShed id": "goseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq", - "Galaxy wrapper version": "1.50.0", - "Conda id": "bioconductor-goseq", - "Conda version": "1.54.0", - "EDAM operation (no superclasses)": [ - "Gene functional annotation" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gprofiler", - "Galaxy tool ids": [ - "gprofiler_convert", - "gprofiler_gost", - "gprofiler_orth", - "gprofiler_random", - "gprofiler_snpense" - ], - "Description": "functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://biit.cs.ut.ee/gprofiler", - "ToolShed categories": [ - "Statistics", - "Web Services" - ], - "ToolShed id": "gprofiler", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler", - "Galaxy wrapper version": "@TOOL_VERSION@+galaxy11", - "Conda id": "r-gprofiler2", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphembed", - "Galaxy tool ids": [ - "graphembed" - ], - "Description": "Compute a 2D embedding of a data matrix given supervised class information", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/fabriziocosta/GraphEmbed", - "ToolShed categories": [ - "Statistics", - "Graphics" - ], - "ToolShed id": "graphembed", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed", - "Galaxy wrapper version": "2.4", - "Conda id": "graph_embed", - "Conda version": "2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "graphlan", - "Galaxy tool ids": [ - "graphlan", - "graphlan_annotate" - ], - "Description": "GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees", - "bio.tool id": "graphlan", - "bio.tool ids": [ - "graphlan" - ], - "biii": null, - "bio.tool name": "GraPhlAn", - "bio.tool description": "GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.", - "EDAM operation": [ - "Phylogenetic inference", - "Phylogenetic tree visualisation", - "Phylogenetic tree editing", - "Taxonomic classification" - ], - "EDAM topic": [ - "Metagenomics", - "Phylogenetics", - "Phylogenomics", - "Cladistics" - ], - "Status": "To update", - "Source": "https://github.com/biobakery/graphlan", - "ToolShed categories": [ - "Metagenomics", - "Graphics", - "Phylogenetics" - ], - "ToolShed id": "graphlan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan", - "Galaxy wrapper version": null, - "Conda id": "graphlan", - "Conda version": "1.1.3", - "EDAM operation (no superclasses)": [ - "Phylogenetic inference", - "Phylogenetic tree visualisation", - "Phylogenetic tree editing", - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Phylogenetics", - "Phylogenomics", - "Cladistics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "gtdbtk", - "Galaxy tool ids": [ - "gtdbtk_classify_wf" - ], - "Description": "GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. ", - "bio.tool id": "GTDB-Tk", - "bio.tool ids": [ - "GTDB-Tk" - ], - "biii": null, - "bio.tool name": "GTDB-Tk", - "bio.tool description": "a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).", - "EDAM operation": [ - "Genome alignment", - "Taxonomic classification", - "Sequence assembly", - "Query and retrieval" - ], - "EDAM topic": [ - "Metagenomics", - "Taxonomy", - "Phylogenetics", - "Database management", - "Proteins" - ], - "Status": "To update", - "Source": "https://github.com/Ecogenomics/GTDBTk", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "gtdbtk", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk", - "Galaxy wrapper version": "2.3.2", - "Conda id": "gtdbtk", - "Conda version": "2.4.0", - "EDAM operation (no superclasses)": [ - "Genome alignment", - "Taxonomic classification", - "Sequence assembly", - "Query and retrieval" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Taxonomy", - "Phylogenetics", - "Database management", - "Proteins" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gtfToBed12", - "Galaxy tool ids": [ - "gtftobed12" - ], - "Description": "Convert GTF files to BED12 format", - "bio.tool id": "UCSC_Genome_Browser_Utilities", - "bio.tool ids": [ - "UCSC_Genome_Browser_Utilities" - ], - "biii": null, - "bio.tool name": "UCSC Genome Browser Utilities", - "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "gtftobed12", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12", - "Galaxy wrapper version": "357", - "Conda id": "ucsc-gtftogenepred", - "Conda version": "447", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "gubbins", - "Galaxy tool ids": [ - "gubbins" - ], - "Description": "Gubbins - bacterial recombination detection", - "bio.tool id": "gubbins", - "bio.tool ids": [ - "gubbins" - ], - "biii": null, - "bio.tool name": "Gubbins", - "bio.tool description": "Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.", - "EDAM operation": [ - "Genotyping", - "Phylogenetic inference", - "Ancestral reconstruction" - ], - "EDAM topic": [ - "Phylogeny", - "Genotype and phenotype", - "Whole genome sequencing" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gubbins", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins", - "Galaxy wrapper version": "3.2.1", - "Conda id": "gubbins", - "Conda version": "3.3.5", - "EDAM operation (no superclasses)": [ - "Genotyping", - "Phylogenetic inference", - "Ancestral reconstruction" - ], - "EDAM topic (no superclasses)": [ - "Phylogeny", - "Genotype and phenotype", - "Whole genome sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gvcftools", - "Galaxy tool ids": [ - "gvcftools_extract_variants" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/sequencing/gvcftools", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools", - "Galaxy wrapper version": "0.1", - "Conda id": "gvcftools", - "Conda version": "0.17.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gwastools", - "Galaxy tool ids": [ - "gwastools_manhattan_plot" - ], - "Description": null, - "bio.tool id": "gwastools", - "bio.tool ids": [ - "gwastools" - ], - "biii": null, - "bio.tool name": "GWASTools", - "bio.tool description": "Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.", - "EDAM operation": [ - "Deposition", - "Analysis", - "Annotation" - ], - "EDAM topic": [ - "GWAS study" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/GWASTools.html", - "ToolShed categories": [ - "Visualization", - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools", - "Galaxy wrapper version": "0.1.0", - "Conda id": "bioconductor-gwastools", - "Conda version": "1.48.0", - "EDAM operation (no superclasses)": [ - "Deposition", - "Analysis", - "Annotation" - ], - "EDAM topic (no superclasses)": [ - "GWAS study" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hamronization", - "Galaxy tool ids": [ - "hamronize_summarize", - "hamronize_tool" - ], - "Description": "Convert AMR gene detection tool output to hAMRonization specification format.", - "bio.tool id": "hamronization", - "bio.tool ids": [ - "hamronization" - ], - "biii": null, - "bio.tool name": "hAMRonization", - "bio.tool description": "Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure", - "EDAM operation": [ - "Data handling", - "Antimicrobial resistance prediction", - "Parsing" - ], - "EDAM topic": [ - "Public health and epidemiology", - "Microbiology", - "Bioinformatics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pha4ge/hAMRonization", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "hamronization", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization", - "Galaxy wrapper version": "1.1.4", - "Conda id": "hamronization", - "Conda version": "1.1.4", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction", - "Parsing" - ], - "EDAM topic (no superclasses)": [ - "Public health and epidemiology", - "Microbiology", - "Bioinformatics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "hansel", - "Galaxy tool ids": [ - "bio_hansel" - ], - "Description": "Heidelberg and Enteritidis SNP Elucidation", - "bio.tool id": "Biohansel", - "bio.tool ids": [ - "Biohansel" - ], - "biii": null, - "bio.tool name": "BioHansel", - "bio.tool description": "BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.", - "EDAM operation": [ - "Genotyping", - "SNP detection", - "Genome assembly" - ], - "EDAM topic": [ - "Whole genome sequencing", - "DNA polymorphism", - "Genotype and phenotype", - "Infectious disease", - "Agricultural science" - ], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/bio_hansel", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "bio_hansel", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel", - "Galaxy wrapper version": "2.6.1", - "Conda id": "bio_hansel", - "Conda version": "2.6.1", - "EDAM operation (no superclasses)": [ - "Genotyping", - "SNP detection", - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "DNA polymorphism", - "Genotype and phenotype", - "Infectious disease", - "Agricultural science" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hapcut2", - "Galaxy tool ids": [ - "hapcut2" - ], - "Description": "Robust and accurate haplotype assembly for diverse sequencing technologies", - "bio.tool id": "hapcut2", - "bio.tool ids": [ - "hapcut2" - ], - "biii": null, - "bio.tool name": "HapCUT2", - "bio.tool description": "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to \"just work\" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md", - "EDAM operation": [ - "Haplotype mapping", - "Variant classification" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/vibansal/HapCUT2", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hapcut2", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2", - "Galaxy wrapper version": "1.3.4", - "Conda id": "hapcut2", - "Conda version": "1.3.4", - "EDAM operation (no superclasses)": [ - "Haplotype mapping", - "Variant classification" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hapog", - "Galaxy tool ids": [ - "hapog" - ], - "Description": "Hapo-G - Haplotype-Aware Polishing of Genomes", - "bio.tool id": "hapog", - "bio.tool ids": [ - "hapog" - ], - "biii": null, - "bio.tool name": "Hapo-G", - "bio.tool description": "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.", - "EDAM operation": [ - "Genome assembly", - "Optimisation and refinement" - ], - "EDAM topic": [ - "Sequence assembly", - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/institut-de-genomique/HAPO-G", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hapog", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog", - "Galaxy wrapper version": "1.3.8", - "Conda id": "hapog", - "Conda version": "1.3.8", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Optimisation and refinement" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "happy", - "Galaxy tool ids": [ - "som.py" - ], - "Description": "A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.", - "bio.tool id": "hap.py", - "bio.tool ids": [ - "hap.py" - ], - "biii": null, - "bio.tool name": "hap.py", - "bio.tool description": "This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.", - "EDAM operation": [ - "Variant calling", - "Sequence analysis", - "Genotyping" - ], - "EDAM topic": [ - "Genomics", - "DNA polymorphism" - ], - "Status": "To update", - "Source": "https://github.com/Illumina/hap.py", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "happy", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy", - "Galaxy wrapper version": "0.3.14", - "Conda id": "hap.py", - "Conda version": "0.3.15", - "EDAM operation (no superclasses)": [ - "Variant calling", - "Sequence analysis", - "Genotyping" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "DNA polymorphism" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "heatmap2", - "Galaxy tool ids": [ - "ggplot2_heatmap2" - ], - "Description": "heatmap.2 function from the R gplots package", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/cran/gplots", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "ggplot2_heatmap2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2", - "Galaxy wrapper version": "3.1.3.1", - "Conda id": "r-gplots", - "Conda version": "2.17.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "heinz", - "Galaxy tool ids": [ - "heinz_bum", - "heinz", - "heinz_scoring", - "heinz_visualization" - ], - "Description": "An algorithm for identification of the optimal scoring subnetwork.", - "bio.tool id": "heinz", - "bio.tool ids": [ - "heinz", - "bionet" - ], - "biii": null, - "bio.tool name": "Heinz", - "bio.tool description": "Tool for single-species active module discovery.", - "EDAM operation": [ - "Pathway or network analysis" - ], - "EDAM topic": [ - "Genetics", - "Gene expression", - "Molecular interactions, pathways and networks" - ], - "Status": "To update", - "Source": "https://github.com/ls-cwi/heinz", - "ToolShed categories": [ - "Transcriptomics", - "Visualization", - "Statistics" - ], - "ToolShed id": "heinz", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz", - "Galaxy wrapper version": "1.0", - "Conda id": "bioconductor-bionet", - "Conda version": "1.62.0", - "EDAM operation (no superclasses)": [ - "Pathway or network analysis" - ], - "EDAM topic (no superclasses)": [ - "Genetics", - "Gene expression", - "Molecular interactions, pathways and networks" - ], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hicexplorer", - "Galaxy tool ids": [ - "hicexplorer_chicaggregatestatistic", - "hicexplorer_chicdifferentialtest", - "hicexplorer_chicexportdata", - "hicexplorer_chicplotviewpoint", - "hicexplorer_chicqualitycontrol", - "hicexplorer_chicsignificantinteractions", - "hicexplorer_chicviewpoint", - "hicexplorer_chicviewpointbackgroundmodel", - "hicexplorer_hicadjustmatrix", - "hicexplorer_hicaggregatecontacts", - "hicexplorer_hicaverageregions", - "hicexplorer_hicbuildmatrix", - "hicexplorer_hiccomparematrices", - "hicexplorer_hiccompartmentspolarization", - "hicexplorer_hicconvertformat", - "hicexplorer_hiccorrectmatrix", - "hicexplorer_hiccorrelate", - "hicexplorer_hicdetectloops", - "hicexplorer_hicdifferentialtad", - "hicexplorer_hicfindrestrictionsites", - "hicexplorer_hicfindtads", - "hicexplorer_hichyperoptDetectLoops", - "hicexplorer_hicinfo", - "hicexplorer_hicinterintratad", - "hicexplorer_hicmergedomains", - "hicexplorer_hicmergeloops", - "hicexplorer_hicmergematrixbins", - "hicexplorer_hicnormalize", - "hicexplorer_hicpca", - "hicexplorer_hicplotaverageregions", - "hicexplorer_hicplotdistvscounts", - "hicexplorer_hicplotmatrix", - "hicexplorer_hicplotsvl", - "hicexplorer_hicplotviewpoint", - "hicexplorer_hicquickqc", - "hicexplorer_hicsummatrices", - "hicexplorer_hictadclassifier", - "hicexplorer_hictraintadclassifier", - "hicexplorer_hictransform", - "hicexplorer_hicvalidatelocations" - ], - "Description": "HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/deeptools/HiCExplorer", - "ToolShed categories": [ - "Sequence Analysis", - "Visualization" - ], - "ToolShed id": "hicexplorer", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer", - "Galaxy wrapper version": "3.7.2", - "Conda id": "hicexplorer", - "Conda version": "3.7.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 40, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "hicstuff", - "Galaxy tool ids": [ - "hicstuff_pipeline" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/koszullab/hicstuff", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff", - "Galaxy wrapper version": "3.1.5", - "Conda id": "hicstuff", - "Conda version": "3.2.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hifiasm_meta", - "Galaxy tool ids": [ - "hifiasm_meta" - ], - "Description": "A hifiasm fork for metagenome assembly using Hifi reads.", - "bio.tool id": "hifiasm-meta", - "bio.tool ids": [ - "hifiasm-meta" - ], - "biii": null, - "bio.tool name": "Hifiasm-meta", - "bio.tool description": "Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.", - "EDAM operation": [ - "Sequence assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Metagenomics" - ], - "Status": "To update", - "Source": "https://github.com/xfengnefx/hifiasm-meta", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "hifiasm_meta", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta", - "Galaxy wrapper version": "0.3.1", - "Conda id": "hifiasm_meta", - "Conda version": "hamtv0.3.1", - "EDAM operation (no superclasses)": [ - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hisat2", - "Galaxy tool ids": [ - "hisat2" - ], - "Description": "HISAT2 is a fast and sensitive spliced alignment program.", - "bio.tool id": "hisat2", - "bio.tool ids": [ - "hisat2" - ], - "biii": null, - "bio.tool name": "HISAT2", - "bio.tool description": "Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "RNA-seq" - ], - "Status": "Up-to-date", - "Source": "http://ccb.jhu.edu/software/hisat2/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hisat2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2", - "Galaxy wrapper version": "2.2.1", - "Conda id": "hisat2", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "hivclustering", - "Galaxy tool ids": [ - "hivclustering" - ], - "Description": "Infers transmission networks from pairwise distances inferred by tn93", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pypi.org/project/hivclustering/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "hivclustering", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering", - "Galaxy wrapper version": "1.3.1", - "Conda id": "python-hivclustering", - "Conda version": "1.6.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hmmer3", - "Galaxy tool ids": [ - "hmmer_alimask", - "hmmer_hmmalign", - "hmmer_hmmbuild", - "hmmer_hmmconvert", - "hmmer_hmmemit", - "hmmer_hmmfetch", - "hmmer_hmmscan", - "hmmer_hmmsearch", - "hmmer_jackhmmer", - "hmmer_nhmmer", - "hmmer_nhmmscan", - "hmmer_phmmer" - ], - "Description": "HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).", - "bio.tool id": "hmmer3", - "bio.tool ids": [ - "hmmer3" - ], - "biii": null, - "bio.tool name": "HMMER3", - "bio.tool description": "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.", - "EDAM operation": [ - "Formatting", - "Multiple sequence alignment", - "Sequence profile generation", - "Format validation", - "Conversion", - "Sequence generation", - "Data retrieval", - "Statistical calculation", - "Database search", - "Formatting", - "Database search", - "Database search", - "Probabilistic sequence generation", - "Statistical calculation", - "Statistical calculation", - "Sequence database search", - "Formatting", - "Sequence database search", - "Database search", - "Sequence database search" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequence sites, features and motifs", - "Gene and protein families" - ], - "Status": "Up-to-date", - "Source": "http://hmmer.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3", - "Galaxy wrapper version": "3.4", - "Conda id": "hmmer", - "Conda version": "3.4", - "EDAM operation (no superclasses)": [ - "Formatting", - "Multiple sequence alignment", - "Sequence profile generation", - "Format validation", - "Conversion", - "Data retrieval", - "Statistical calculation", - "Formatting", - "Probabilistic sequence generation", - "Statistical calculation", - "Statistical calculation", - "Sequence database search", - "Formatting", - "Sequence database search", - "Sequence database search" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Sequence sites, features and motifs", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 12, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "homer", - "Galaxy tool ids": [ - "homer_annotatePeaks", - "homer_findMotifs", - "homer_findMotifsGenome", - "homer_gtf_to_annotations", - "homer_scanMotifGenomeWide" - ], - "Description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.", - "bio.tool id": "homer", - "bio.tool ids": [ - "homer" - ], - "biii": null, - "bio.tool name": "homer", - "bio.tool description": "HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.", - "EDAM operation": [ - "Sequence motif discovery" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://homer.ucsd.edu/homer/index.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "data_manager_homer_preparse", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer", - "Galaxy wrapper version": "4.11", - "Conda id": "homer", - "Conda version": "4.11", - "EDAM operation (no superclasses)": [ - "Sequence motif discovery" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "htseq_count", - "Galaxy tool ids": [ - "htseq_count" - ], - "Description": "Count aligned reads (SAM/BAM) that overlap genomic features (GFF)", - "bio.tool id": "htseq", - "bio.tool ids": [ - "htseq" - ], - "biii": null, - "bio.tool name": "HTSeq", - "bio.tool description": "Python framework to process and analyse high-throughput sequencing (HTS) data", - "EDAM operation": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://readthedocs.org/projects/htseq/", - "ToolShed categories": [ - "Genomic Interval Operations", - "SAM", - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "htseq_count", - "Galaxy wrapper owner": "lparsons", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count", - "Galaxy wrapper version": "2.0.5", - "Conda id": "htseq", - "Conda version": "2.0.5", - "EDAM operation (no superclasses)": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "humann", - "Galaxy tool ids": [ - "humann", - "humann_associate", - "humann_barplot", - "humann_join_tables", - "humann_reduce_table", - "humann_regroup_table", - "humann_rename_table", - "humann_renorm_table", - "humann_rna_dna_norm", - "humann_split_stratified_table", - "humann_split_table", - "humann_strain_profiler", - "humann_unpack_pathways" - ], - "Description": "HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution", - "bio.tool id": "humann", - "bio.tool ids": [ - "humann" - ], - "biii": null, - "bio.tool name": "humann", - "bio.tool description": "HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”", - "EDAM operation": [ - "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" - ], - "EDAM topic": [ - "Metagenomics", - "Phylogenomics" - ], - "Status": "Up-to-date", - "Source": "http://huttenhower.sph.harvard.edu/humann", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "humann", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann", - "Galaxy wrapper version": "3.8", - "Conda id": "humann", - "Conda version": "3.8", - "EDAM operation (no superclasses)": [ - "Species frequency estimation", - "Taxonomic classification", - "Phylogenetic analysis" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Phylogenomics" - ], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 13, - "Available on UseGalaxy.org.fr": 13 - }, - { - "Galaxy wrapper id": "hybpiper", - "Galaxy tool ids": [ - "hybpiper" - ], - "Description": "Analyse targeted sequence capture data", - "bio.tool id": "HybPiper", - "bio.tool ids": [ - "HybPiper" - ], - "biii": null, - "bio.tool name": "HybPiper", - "bio.tool description": "Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.", - "EDAM operation": [ - "Sequence trimming", - "Sequence assembly", - "Read mapping" - ], - "EDAM topic": [ - "Phylogenetics", - "Plant biology", - "Gene transcripts", - "Sequence assembly", - "Phylogenomics" - ], - "Status": "To update", - "Source": "https://github.com/mossmatters/HybPiper", - "ToolShed categories": [ - "Sequence Analysis", - "Phylogenetics" - ], - "ToolShed id": "hybpiper", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper", - "Galaxy wrapper version": "2.1.6", - "Conda id": "hybpiper", - "Conda version": "2.1.7", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "Sequence assembly", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics", - "Plant biology", - "Gene transcripts", - "Sequence assembly", - "Phylogenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hyphy", - "Galaxy tool ids": [ - "hyphy_absrel", - "hyphy_annotate", - "hyphy_bgm", - "hyphy_busted", - "hyphy_cfel", - "hyphy_conv", - "hyphy_fade", - "hyphy_fel", - "hyphy_fubar", - "hyphy_gard", - "hyphy_meme", - "hyphy_prime", - "hyphy_relax", - "hyphy_slac", - "hyphy_sm19", - "hyphy_strike_ambigs", - "hyphy_summary" - ], - "Description": "Hypothesis Testing using Phylogenies", - "bio.tool id": "HyPhy", - "bio.tool ids": [ - "HyPhy" - ], - "biii": null, - "bio.tool name": "HyPhy", - "bio.tool description": "Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.", - "EDAM operation": [ - "Statistical calculation" - ], - "EDAM topic": [ - "Phylogeny", - "Small molecules", - "Molecular interactions, pathways and networks" - ], - "Status": "To update", - "Source": "http://www.hyphy.org", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy", - "Galaxy wrapper version": "2.5.47", - "Conda id": "hyphy", - "Conda version": "2.5.62", - "EDAM operation (no superclasses)": [ - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Phylogeny", - "Small molecules", - "Molecular interactions, pathways and networks" - ], - "Available on UseGalaxy.org": 17, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 17, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "hypo", - "Galaxy tool ids": [ - "hypo" - ], - "Description": "Super Fast & Accurate Polisher for Long Read Genome Assemblies", - "bio.tool id": "HyPo", - "bio.tool ids": [ - "HyPo" - ], - "biii": null, - "bio.tool name": "HyPo", - "bio.tool description": "HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.", - "EDAM operation": [ - "Optimisation and refinement", - "Genome assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/kensung-lab/hypo", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "hypo", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo", - "Galaxy wrapper version": "1.0.3", - "Conda id": "hypo", - "Conda version": "1.0.3", - "EDAM operation (no superclasses)": [ - "Optimisation and refinement", - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "icescreen", - "Galaxy tool ids": [ - "icescreen" - ], - "Description": "ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.", - "bio.tool id": "icescreen", - "bio.tool ids": [ - "icescreen" - ], - "biii": null, - "bio.tool name": "ICEscreen", - "bio.tool description": "A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.", - "EDAM operation": [ - "Database search", - "Protein feature detection" - ], - "EDAM topic": [ - "Mobile genetic elements", - "Sequence sites, features and motifs", - "Genomics", - "Molecular interactions, pathways and networks", - "Structural variation" - ], - "Status": "To update", - "Source": "https://icescreen.migale.inrae.fr/", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "icescreen", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://forgemia.inra.fr/ices_imes_analysis/icescreen", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen", - "Galaxy wrapper version": "1.3.1", - "Conda id": "icescreen", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [ - "Database search", - "Protein feature detection" - ], - "EDAM topic (no superclasses)": [ - "Mobile genetic elements", - "Sequence sites, features and motifs", - "Genomics", - "Molecular interactions, pathways and networks", - "Structural variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "idba_ud", - "Galaxy tool ids": [ - "idba_hybrid", - "idba_tran", - "idba_ud" - ], - "Description": "Wrappers for the idba assembler variants.", - "bio.tool id": "idba", - "bio.tool ids": [ - "idba" - ], - "biii": null, - "bio.tool name": "IDBA", - "bio.tool description": "A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.", - "EDAM operation": [ - "Sequence assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://i.cs.hku.hk/~alse/hkubrg/projects/index.html", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "idba", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud", - "Galaxy wrapper version": null, - "Conda id": "idba", - "Conda version": "1.1.3", - "EDAM operation (no superclasses)": [ - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "idr", - "Galaxy tool ids": [ - "idr" - ], - "Description": "Galaxy wrappers for the IDR package from Nathan Boleu", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nboley/idr", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "idr", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr", - "Galaxy wrapper version": "2.0.3", - "Conda id": "idr", - "Conda version": "2.0.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "idr_download", - "Galaxy tool ids": [ - "idr_download_by_ids" - ], - "Description": "Image Data Resource downloading tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://idr.openmicroscopy.org", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "idr_download_by_ids", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download", - "Galaxy wrapper version": "0.44.1", - "Conda id": "omero-py", - "Conda version": "5.11.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "iedb_api", - "Galaxy tool ids": [ - "iedb_api" - ], - "Description": "Get epitope binding predictions from IEDB-API", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://tools.immuneepitope.org/main/tools-api/", - "ToolShed categories": [ - "Data Source", - "Sequence Analysis" - ], - "ToolShed id": "iedb_api", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api", - "Galaxy wrapper version": "2.15.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "instrain", - "Galaxy tool ids": [ - "instrain_compare", - "instrain_profile" - ], - "Description": "InStrain is a tool for analysis of co-occurring genome populations from metagenomes", - "bio.tool id": "instrain", - "bio.tool ids": [ - "instrain" - ], - "biii": null, - "bio.tool name": "InStrain", - "bio.tool description": "InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification", - "EDAM operation": [ - "SNP detection", - "Genome comparison" - ], - "EDAM topic": [ - "Mapping", - "Metagenomics" - ], - "Status": "To update", - "Source": "https://instrain.readthedocs.io/en/latest/#", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "instrain", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain", - "Galaxy wrapper version": "1.5.3", - "Conda id": "instrain", - "Conda version": "1.9.0", - "EDAM operation (no superclasses)": [ - "SNP detection", - "Genome comparison" - ], - "EDAM topic (no superclasses)": [ - "Mapping", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "integron_finder", - "Galaxy tool ids": [ - "integron_finder" - ], - "Description": "\"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching\"", - "bio.tool id": "integron_finder", - "bio.tool ids": [ - "integron_finder" - ], - "biii": null, - "bio.tool name": "Integron Finder", - "bio.tool description": "A tool to detect Integron in DNA sequences.", - "EDAM operation": [ - "Nucleic acid feature detection", - "Sequence motif recognition", - "Protein feature detection", - "Genome annotation" - ], - "EDAM topic": [ - "Functional genomics", - "Mobile genetic elements", - "Molecular biology", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/gem-pasteur/Integron_Finder", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "integronfinder", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder", - "Galaxy wrapper version": "2.0.3", - "Conda id": "integron_finder", - "Conda version": "2.0.3", - "EDAM operation (no superclasses)": [ - "Nucleic acid feature detection", - "Sequence motif recognition", - "Protein feature detection", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Functional genomics", - "Mobile genetic elements", - "Molecular biology", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "intermine_galaxy_exchange", - "Galaxy tool ids": [ - "galaxy_intermine_exchange" - ], - "Description": "InterMine Exporter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "intermine_galaxy_exchange", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange", - "Galaxy wrapper version": "0.0.1", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "interproscan", - "Galaxy tool ids": [ - "interproscan" - ], - "Description": "Interproscan queries the interpro database and provides annotations.", - "bio.tool id": "interproscan_ebi", - "bio.tool ids": [ - "interproscan_ebi" - ], - "biii": null, - "bio.tool name": "InterProScan (EBI)", - "bio.tool description": "Scan sequences against the InterPro protein signature databases.", - "EDAM operation": [ - "Sequence motif recognition", - "Protein feature detection" - ], - "EDAM topic": [ - "Gene and protein families", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.ebi.ac.uk/Tools/pfa/iprscan5/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "interproscan", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan", - "Galaxy wrapper version": "5.59-91.0", - "Conda id": "interproscan", - "Conda version": "5.59_91.0", - "EDAM operation (no superclasses)": [ - "Sequence motif recognition", - "Protein feature detection" - ], - "EDAM topic (no superclasses)": [ - "Gene and protein families", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "interval2maf", - "Galaxy tool ids": [ - "Interval2Maf1" - ], - "Description": "Extract MAF blocks given a set of intervals", - "bio.tool id": "bx-python", - "bio.tool ids": [ - "bx-python" - ], - "biii": null, - "bio.tool name": "bx-python", - "bio.tool description": "Tools for manipulating biological data, particularly multiple sequence alignments.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "interval2maf", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf", - "Galaxy wrapper version": "1.0.1+galaxy1", - "Conda id": "bx-python", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "intervene", - "Galaxy tool ids": [ - "intervene_pairwise", - "intervene_upset" - ], - "Description": "Create pairwise and upset plots", - "bio.tool id": "intervene", - "bio.tool ids": [ - "intervene" - ], - "biii": null, - "bio.tool name": "Intervene", - "bio.tool description": "Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.", - "EDAM operation": [ - "Sequence comparison", - "Sequence visualisation" - ], - "EDAM topic": [ - "Computational biology" - ], - "Status": "Up-to-date", - "Source": "https://intervene.readthedocs.io", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "intervene", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene", - "Galaxy wrapper version": "0.6.5", - "Conda id": "intervene", - "Conda version": "0.6.5", - "EDAM operation (no superclasses)": [ - "Sequence comparison", - "Sequence visualisation" - ], - "EDAM topic (no superclasses)": [ - "Computational biology" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "iqtree", - "Galaxy tool ids": [ - "iqtree" - ], - "Description": "Efficient phylogenomic software by maximum likelihood", - "bio.tool id": "iqtree", - "bio.tool ids": [ - "iqtree" - ], - "biii": null, - "bio.tool name": "iqtree", - "bio.tool description": "A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time", - "EDAM operation": [ - "Phylogenetic analysis", - "Sequence analysis" - ], - "EDAM topic": [ - "Phylogenetics" - ], - "Status": "Up-to-date", - "Source": "http://www.iqtree.org/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "iqtree", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree", - "Galaxy wrapper version": "2.3.4", - "Conda id": "iqtree", - "Conda version": "2.3.4", - "EDAM operation (no superclasses)": [ - "Phylogenetic analysis", - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "irissv", - "Galaxy tool ids": [ - "irissv" - ], - "Description": "Refine insertion sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/mkirsche/Iris", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "irissv", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/irissv/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv", - "Galaxy wrapper version": "1.0.5", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "isescan", - "Galaxy tool ids": [ - "isescan" - ], - "Description": "\"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.\"", - "bio.tool id": "ISEScan", - "bio.tool ids": [ - "ISEScan" - ], - "biii": null, - "bio.tool name": "ISEScan", - "bio.tool description": "Automated identification of insertion sequence elements in prokaryotic genomes.", - "EDAM operation": [ - "Structural variation detection" - ], - "EDAM topic": [ - "Genomics", - "DNA structural variation", - "Sequence analysis", - "Genetic variation" - ], - "Status": "To update", - "Source": "https://github.com/xiezhq/ISEScan", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ISEScan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan", - "Galaxy wrapper version": "1.7.2.3", - "Conda id": "isescan", - "Conda version": "1.7.2.1", - "EDAM operation (no superclasses)": [ - "Structural variation detection" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence analysis", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "isoformswitchanalyzer", - "Galaxy tool ids": [ - "isoformswitchanalyzer" - ], - "Description": "Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.", - "bio.tool id": "IsoformSwitchAnalyzeR", - "bio.tool ids": [ - "IsoformSwitchAnalyzeR" - ], - "biii": null, - "bio.tool name": "IsoformSwitchAnalyzeR", - "bio.tool description": "Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.", - "EDAM operation": [ - "Sequence comparison", - "Sequence analysis" - ], - "EDAM topic": [ - "Computational biology", - "Gene transcripts" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "isoformswitchanalyzer", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer", - "Galaxy wrapper version": "1.20.0", - "Conda id": "bioconductor-isoformswitchanalyzer", - "Conda version": "2.2.0", - "EDAM operation (no superclasses)": [ - "Sequence comparison", - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Computational biology", - "Gene transcripts" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ivar", - "Galaxy tool ids": [ - "ivar_consensus", - "ivar_filtervariants", - "ivar_removereads", - "ivar_trim", - "ivar_variants" - ], - "Description": "iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/andersen-lab/ivar", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ivar", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar", - "Galaxy wrapper version": "1.4.2", - "Conda id": "ivar", - "Conda version": "1.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "iwtomics", - "Galaxy tool ids": [ - "iwtomics_loadandplot", - "iwtomics_plotwithscale", - "iwtomics_testandplot" - ], - "Description": "Interval-Wise Testing for Omics Data", - "bio.tool id": "iwtomics", - "bio.tool ids": [ - "iwtomics" - ], - "biii": null, - "bio.tool name": "IWTomics", - "bio.tool description": "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in \"Omics\" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.", - "EDAM operation": [ - "Differential gene expression analysis", - "Differentially-methylated region identification", - "Peak calling", - "Genome annotation", - "Comparison" - ], - "EDAM topic": [ - "Statistics and probability" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/IWTomics.html", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "iwtomics", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics", - "Galaxy wrapper version": "1.0.0", - "Conda id": "bioconductor-iwtomics", - "Conda version": "1.26.0", - "EDAM operation (no superclasses)": [ - "Differential gene expression analysis", - "Peak calling", - "Genome annotation", - "Comparison" - ], - "EDAM topic (no superclasses)": [ - "Statistics and probability" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "jasminesv", - "Galaxy tool ids": [ - "jasminesv" - ], - "Description": "Merge structural variants across samples", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/mkirsche/Jasmine/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "jasminesv", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/jasminesv/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv", - "Galaxy wrapper version": "1.0.11", - "Conda id": "jasminesv", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "jbrowse", - "Galaxy tool ids": [ - "jbrowse_to_standalone", - "jbrowse" - ], - "Description": "JBrowse Genome Browser integrated as a Galaxy Tool", - "bio.tool id": "jbrowse", - "bio.tool ids": [ - "jbrowse" - ], - "biii": null, - "bio.tool name": "JBrowse", - "bio.tool description": "Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.", - "EDAM operation": [ - "Genome visualisation" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://jbrowse.org", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "jbrowse", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse", - "Galaxy wrapper version": "1.16.11", - "Conda id": "jbrowse", - "Conda version": "1.16.11", - "EDAM operation (no superclasses)": [ - "Genome visualisation" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "jcvi_gff_stats", - "Galaxy tool ids": [ - "jcvi_gff_stats" - ], - "Description": "Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/tanghaibao/jcvi", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "jcvi_gff_stats", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats", - "Galaxy wrapper version": "0.8.4", - "Conda id": "jcvi", - "Conda version": "1.4.15", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "jellyfish", - "Galaxy tool ids": [ - "jellyfish" - ], - "Description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA", - "bio.tool id": "Jellyfish", - "bio.tool ids": [ - "Jellyfish" - ], - "biii": null, - "bio.tool name": "Jellyfish", - "bio.tool description": "A command-line algorithm for counting k-mers in DNA sequence.", - "EDAM operation": [ - "k-mer counting" - ], - "EDAM topic": [ - "Sequence analysis", - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/gmarcais/Jellyfish", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "jellyfish", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish", - "Galaxy wrapper version": null, - "Conda id": "kmer-jellyfish", - "Conda version": "2.3.1", - "EDAM operation (no superclasses)": [ - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "join_files_by_id", - "Galaxy tool ids": [ - "join_files_by_id" - ], - "Description": "This tool will join datasets according to a column with identifier", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "join_files_by_id", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id", - "Galaxy wrapper version": "1.0", - "Conda id": "r-data.table", - "Conda version": "1.11.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "jq", - "Galaxy tool ids": [ - "jq" - ], - "Description": "JQ is a lightweight and flexible command-line JSON processor", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://stedolan.github.io/jq/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "jq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq", - "Galaxy wrapper version": "1.0", - "Conda id": "jq", - "Conda version": "1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "jvarkit", - "Galaxy tool ids": [ - "jvarkit_wgscoverageplotter" - ], - "Description": "Jvarkit : Java utilities for Bioinformatics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://lindenb.github.io/jvarkit/", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "jvarkit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit", - "Galaxy wrapper version": "20201223", - "Conda id": "jvarkit-wgscoverageplotter", - "Conda version": "20201223", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kallisto", - "Galaxy tool ids": [ - "kallisto_pseudo", - "kallisto_quant" - ], - "Description": "kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.", - "bio.tool id": "kallisto", - "bio.tool ids": [ - "kallisto" - ], - "biii": null, - "bio.tool name": "kallisto", - "bio.tool description": "A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.", - "EDAM operation": [ - "Gene expression profiling" - ], - "EDAM topic": [ - "Transcriptomics", - "RNA-seq", - "Gene expression" - ], - "Status": "To update", - "Source": "https://pachterlab.github.io/kallisto/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto", - "Galaxy wrapper version": "0.48.0", - "Conda id": "kallisto", - "Conda version": "0.50.1", - "EDAM operation (no superclasses)": [ - "Gene expression profiling" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "kc-align", - "Galaxy tool ids": [ - "kc-align" - ], - "Description": "Kc-Align custom tool", - "bio.tool id": "kc-align", - "bio.tool ids": [ - "kc-align" - ], - "biii": null, - "bio.tool name": "kc-align", - "bio.tool description": "A fast and accurate tool for performing codon-aware multiple sequence alignments", - "EDAM operation": [ - "Multiple sequence alignment" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/davebx/kc-align", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "kc_align", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align", - "Galaxy wrapper version": "1.0.2", - "Conda id": "kcalign", - "Conda version": "1.0.2", - "EDAM operation (no superclasses)": [ - "Multiple sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "khmer", - "Galaxy tool ids": [ - "khmer_abundance_distribution_single", - "khmer_abundance_distribution", - "khmer_count_median", - "khmer_partition", - "khmer_extract_partitions", - "khmer_filter_abundance", - "khmer_filter_below_abundance_cutoff", - "khmer_normalize_by_median" - ], - "Description": "In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more", - "bio.tool id": "khmer", - "bio.tool ids": [ - "khmer" - ], - "biii": null, - "bio.tool name": "khmer", - "bio.tool description": "khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.", - "EDAM operation": [ - "Standardisation and normalisation", - "De-novo assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://khmer.readthedocs.org/", - "ToolShed categories": [ - "Assembly", - "Next Gen Mappers" - ], - "ToolShed id": "khmer", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer", - "Galaxy wrapper version": "3.0.0a3", - "Conda id": "khmer", - "Conda version": "3.0.0a3", - "EDAM operation (no superclasses)": [ - "Standardisation and normalisation", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 8, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "king", - "Galaxy tool ids": [ - "king" - ], - "Description": "Kinship-based INference for Gwas", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://people.virginia.edu/~wc9c/KING/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "king", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/king", - "Galaxy wrapper version": "2.2.7", - "Conda id": "king", - "Conda version": "2.2.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kleborate", - "Galaxy tool ids": [ - "kleborate" - ], - "Description": "Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)", - "bio.tool id": "kleborate", - "bio.tool ids": [ - "kleborate" - ], - "biii": null, - "bio.tool name": "Kleborate", - "bio.tool description": "Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).", - "EDAM operation": [ - "Multilocus sequence typing", - "Genome assembly", - "Virulence prediction" - ], - "EDAM topic": [ - "Public health and epidemiology", - "Metagenomics", - "Population genomics", - "Sequence assembly", - "Whole genome sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/katholt/Kleborate/wiki", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kleborate", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/katholt/Kleborate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate", - "Galaxy wrapper version": "2.3.2", - "Conda id": "kleborate", - "Conda version": "2.3.2", - "EDAM operation (no superclasses)": [ - "Multilocus sequence typing", - "Genome assembly", - "Virulence prediction" - ], - "EDAM topic (no superclasses)": [ - "Public health and epidemiology", - "Metagenomics", - "Population genomics", - "Sequence assembly", - "Whole genome sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kma", - "Galaxy tool ids": [ - "kma_map" - ], - "Description": "Map with KMA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/genomicepidemiology/kma", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "kma", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma", - "Galaxy wrapper version": "1.2.21", - "Conda id": "kma", - "Conda version": "1.4.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "kofamscan", - "Galaxy tool ids": [ - "kofamscan" - ], - "Description": "Gene function annotation tool based on KEGG Orthology and hidden Markov model", - "bio.tool id": "kofamscan", - "bio.tool ids": [ - "kofamscan" - ], - "biii": null, - "bio.tool name": "kofamscan", - "bio.tool description": "KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.", - "EDAM operation": [ - "Sequence analysis", - "Gene functional annotation" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/takaram/kofam_scan", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "kofamscan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan", - "Galaxy wrapper version": "1.3.0", - "Conda id": "kofamscan", - "Conda version": "1.3.0", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Gene functional annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "kraken_biom", - "Galaxy tool ids": [ - "kraken_biom" - ], - "Description": "Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/smdabdoub/kraken-biom", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kraken_biom", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/smdabdoub/kraken-biom", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom", - "Galaxy wrapper version": "1.2.0", - "Conda id": "kraken-biom", - "Conda version": "1.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "kraken_taxonomy_report", - "Galaxy tool ids": [ - "kraken_taxonomy_report" - ], - "Description": "Kraken taxonomy report", - "bio.tool id": "Kraken-Taxonomy-Report", - "bio.tool ids": [ - "Kraken-Taxonomy-Report" - ], - "biii": null, - "bio.tool name": "Kraken-Taxonomy-Report", - "bio.tool description": "view report of classification for multiple samples", - "EDAM operation": [ - "Visualisation", - "Classification" - ], - "EDAM topic": [ - "Metagenomics", - "Taxonomy" - ], - "Status": "To update", - "Source": "https://github.com/blankenberg/Kraken-Taxonomy-Report", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kraken_taxonomy_report", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report", - "Galaxy wrapper version": "0.0.3", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [ - "Visualisation", - "Classification" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Taxonomy" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "krakentools", - "Galaxy tool ids": [ - "krakentools_alpha_diversity", - "krakentools_beta_diversity", - "krakentools_combine_kreports", - "krakentools_extract_kraken_reads", - "krakentools_kreport2krona", - "krakentools_kreport2mpa" - ], - "Description": "KrakenTools is a suite of scripts to be used alongside the Kraken", - "bio.tool id": "krakentools", - "bio.tool ids": [ - "krakentools" - ], - "biii": null, - "bio.tool name": "KrakenTools", - "bio.tool description": "KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files", - "EDAM operation": [ - "Visualisation", - "Aggregation" - ], - "EDAM topic": [ - "Taxonomy", - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/jenniferlu717/KrakenTools", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "krakentools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools", - "Galaxy wrapper version": "1.2", - "Conda id": "krakentools", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [ - "Visualisation", - "Aggregation" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy", - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "krocus", - "Galaxy tool ids": [ - "krocus" - ], - "Description": "Predict MLST directly from uncorrected long reads", - "bio.tool id": "krocus", - "bio.tool ids": [ - "krocus" - ], - "biii": null, - "bio.tool name": "krocus", - "bio.tool description": "Predict MLST directly from uncorrected long reads", - "EDAM operation": [ - "Multilocus sequence typing", - "k-mer counting" - ], - "EDAM topic": [ - "Public health and epidemiology" - ], - "Status": "To update", - "Source": "https://github.com/quadram-institute-bioscience/krocus", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "krocus", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus", - "Galaxy wrapper version": "1.0.1", - "Conda id": "krocus", - "Conda version": "1.0.3", - "EDAM operation (no superclasses)": [ - "Multilocus sequence typing", - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Public health and epidemiology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "last", - "Galaxy tool ids": [ - "last_al", - "last_db", - "last_split", - "last_train", - "last_maf_convert" - ], - "Description": "LAST finds similar regions between sequences.", - "bio.tool id": "last", - "bio.tool ids": [ - "last" - ], - "biii": null, - "bio.tool name": "LAST", - "bio.tool description": "Short read alignment program incorporating quality scores", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "Genomics", - "Comparative genomics" - ], - "Status": "To update", - "Source": "http://last.cbrc.jp/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "last", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/last", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/last", - "Galaxy wrapper version": "1205", - "Conda id": "last", - "Conda version": "1542", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Comparative genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "lastz", - "Galaxy tool ids": [ - "lastz_wrapper_2", - "lastz_d_wrapper" - ], - "Description": "Galaxy wrappers for the Lastz and Lastz_d", - "bio.tool id": "lastz", - "bio.tool ids": [ - "lastz" - ], - "biii": null, - "bio.tool name": "LASTZ", - "bio.tool description": "A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.", - "EDAM operation": [ - "Sequence alignment", - "Read mapping" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/lastz/lastz", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "lastz", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz", - "Galaxy wrapper version": "1.04.22", - "Conda id": "lastz", - "Conda version": "1.04.22", - "EDAM operation (no superclasses)": [ - "Sequence alignment", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "lcrgenie", - "Galaxy tool ids": [ - "lcrgenie" - ], - "Description": "Ligase Chain Reaction Genie", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/neilswainston/LCRGenie", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "lcrgenie", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie", - "Galaxy wrapper version": "1.0.2", - "Conda id": "lcr_genie", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "legsta", - "Galaxy tool ids": [ - "legsta" - ], - "Description": "Performs in silico Legionella pneumophila sequence based typing.", - "bio.tool id": "legsta", - "bio.tool ids": [ - "legsta" - ], - "biii": null, - "bio.tool name": "legsta", - "bio.tool description": "Performs in silico Legionella pneumophila sequence based typing", - "EDAM operation": [ - "Sequence analysis" - ], - "EDAM topic": [ - "Public health and epidemiology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/tseemann/legsta", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "legsta", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/tseemann/legsta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta", - "Galaxy wrapper version": "0.5.1", - "Conda id": "legsta", - "Conda version": "0.5.1", - "EDAM operation (no superclasses)": [ - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Public health and epidemiology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "length_and_gc_content", - "Galaxy tool ids": [ - "length_and_gc_content" - ], - "Description": "Gets gene length and gc content from a fasta and a GTF file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content", - "ToolShed categories": [ - "Fasta Manipulation", - "Statistics", - "RNA", - "Micro-array Analysis" - ], - "ToolShed id": "length_and_gc_content", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content", - "Galaxy wrapper version": "0.1.2", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "limma_voom", - "Galaxy tool ids": [ - "limma_voom" - ], - "Description": "Perform RNA-Seq differential expression analysis using limma voom pipeline", - "bio.tool id": "limma", - "bio.tool ids": [ - "limma" - ], - "biii": null, - "bio.tool name": "limma", - "bio.tool description": "Data analysis, linear models and differential expression for microarray data.", - "EDAM operation": [ - "RNA-Seq analysis" - ], - "EDAM topic": [ - "Molecular biology", - "Genetics" - ], - "Status": "Up-to-date", - "Source": "http://bioconductor.org/packages/release/bioc/html/limma.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "limma_voom", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom", - "Galaxy wrapper version": "3.58.1", - "Conda id": "bioconductor-limma", - "Conda version": "3.58.1", - "EDAM operation (no superclasses)": [ - "RNA-Seq analysis" - ], - "EDAM topic (no superclasses)": [ - "Molecular biology", - "Genetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "lineagespot", - "Galaxy tool ids": [ - "lineagespot" - ], - "Description": "Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)", - "bio.tool id": "lineagespot", - "bio.tool ids": [ - "lineagespot" - ], - "biii": null, - "bio.tool name": "lineagespot", - "bio.tool description": "Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).", - "EDAM operation": [ - "Variant calling" - ], - "EDAM topic": [ - "Metagenomics", - "Gene transcripts", - "Evolutionary biology", - "Sequencing", - "Genetic variation" - ], - "Status": "To update", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html", - "ToolShed categories": [ - "Metagenomics", - "Sequence Analysis" - ], - "ToolShed id": "lineagespot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot", - "Galaxy wrapper version": "1.6.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Gene transcripts", - "Evolutionary biology", - "Sequencing", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "links", - "Galaxy tool ids": [ - "links" - ], - "Description": "Scaffold genome assemblies with long reads.", - "bio.tool id": "links", - "bio.tool ids": [ - "links" - ], - "biii": null, - "bio.tool name": "LINKS", - "bio.tool description": "LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.", - "EDAM operation": [ - "Scaffolding", - "Genome assembly", - "Read mapping", - "Read pre-processing", - "Sequence trimming" - ], - "EDAM topic": [ - "Sequence assembly", - "Mapping", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/bcgsc/LINKS", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "links", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/links", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/links", - "Galaxy wrapper version": "2.0.1", - "Conda id": "links", - "Conda version": "2.0.1", - "EDAM operation (no superclasses)": [ - "Scaffolding", - "Genome assembly", - "Read mapping", - "Read pre-processing", - "Sequence trimming" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Mapping", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lofreq", - "Galaxy tool ids": [ - "lofreq_alnqual", - "lofreq_call", - "lofreq_filter", - "lofreq_indelqual", - "lofreq_viterbi" - ], - "Description": "LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csb5.github.io/lofreq/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq", - "Galaxy wrapper version": "2.1.5", - "Conda id": "lofreq", - "Conda version": "2.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "lorikeet", - "Galaxy tool ids": [ - "lorikeet_spoligotype" - ], - "Description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", - "bio.tool id": "lorikeet", - "bio.tool ids": [ - "lorikeet" - ], - "biii": null, - "bio.tool name": "lorikeet", - "bio.tool description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", - "EDAM operation": [ - "Sequence analysis", - "Genotyping" - ], - "EDAM topic": [ - "Genotype and phenotype" - ], - "Status": "Up-to-date", - "Source": "https://github.com/AbeelLab/lorikeet", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "lorikeet_spoligotype", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/AbeelLab/lorikeet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet", - "Galaxy wrapper version": "20", - "Conda id": "lorikeet", - "Conda version": "20", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Genotyping" - ], - "EDAM topic (no superclasses)": [ - "Genotype and phenotype" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lumpy_sv", - "Galaxy tool ids": [ - "lumpy_prep", - "lumpy_sv" - ], - "Description": "LUMPY - a general probabilistic framework for structural variant discovery", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://layerlab.org/software/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "lumpy_sv", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/arq5x/lumpy-sv", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv", - "Galaxy wrapper version": "0.3.1", - "Conda id": "lumpy-sv", - "Conda version": "0.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "m6anet", - "Galaxy tool ids": [ - "m6anet" - ], - "Description": "m6anet to detect m6A RNA modifications from nanopore data", - "bio.tool id": "m6Anet", - "bio.tool ids": [ - "m6Anet" - ], - "biii": null, - "bio.tool name": "m6Anet", - "bio.tool description": "Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.", - "EDAM operation": [ - "Quantification", - "Imputation", - "Gene expression profiling" - ], - "EDAM topic": [ - "RNA-Seq", - "Transcriptomics", - "RNA", - "Machine learning" - ], - "Status": "Up-to-date", - "Source": "https://m6anet.readthedocs.io/en/latest", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "m6anet", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet", - "Galaxy wrapper version": "2.1.0", - "Conda id": "m6anet", - "Conda version": "2.1.0", - "EDAM operation (no superclasses)": [ - "Quantification", - "Imputation", - "Gene expression profiling" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Transcriptomics", - "RNA", - "Machine learning" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "maaslin2", - "Galaxy tool ids": [ - "maaslin2" - ], - "Description": "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.", - "bio.tool id": "maaslin2", - "bio.tool ids": [ - "maaslin2" - ], - "biii": null, - "bio.tool name": "MaAsLin2", - "bio.tool description": "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.", - "EDAM operation": [ - "Filtering", - "Statistical calculation", - "Standardisation and normalisation", - "Visualisation" - ], - "EDAM topic": [ - "Metagenomics", - "Statistics and probability" - ], - "Status": "To update", - "Source": "http://huttenhower.sph.harvard.edu/maaslin", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "maaslin2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/biobakery/Maaslin2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2", - "Galaxy wrapper version": "0.99.12", - "Conda id": "maaslin2", - "Conda version": "1.16.0", - "EDAM operation (no superclasses)": [ - "Filtering", - "Standardisation and normalisation", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "macs2", - "Galaxy tool ids": [ - "macs2_bdgbroadcall", - "macs2_bdgcmp", - "macs2_bdgdiff", - "macs2_bdgpeakcall", - "macs2_callpeak", - "macs2_filterdup", - "macs2_predictd", - "macs2_randsample", - "macs2_refinepeak" - ], - "Description": "MACS - Model-based Analysis of ChIP-Seq", - "bio.tool id": "macs", - "bio.tool ids": [ - "macs" - ], - "biii": null, - "bio.tool name": "MACS", - "bio.tool description": "Model-based Analysis of ChIP-seq data.", - "EDAM operation": [ - "Peak calling", - "Enrichment analysis", - "Gene regulatory network analysis" - ], - "EDAM topic": [ - "ChIP-seq", - "Molecular interactions, pathways and networks", - "Transcription factors and regulatory sites" - ], - "Status": "Up-to-date", - "Source": "https://github.com/taoliu/MACS", - "ToolShed categories": [ - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": "macs2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2", - "Galaxy wrapper version": "2.2.9.1", - "Conda id": "macs2", - "Conda version": "2.2.9.1", - "EDAM operation (no superclasses)": [ - "Peak calling", - "Enrichment analysis", - "Gene regulatory network analysis" - ], - "EDAM topic (no superclasses)": [ - "ChIP-seq", - "Molecular interactions, pathways and networks", - "Transcription factors and regulatory sites" - ], - "Available on UseGalaxy.org": 9, - "Available on UseGalaxy.org.au": 9, - "Available on UseGalaxy.eu": 9, - "Available on UseGalaxy.org.fr": 9 - }, - { - "Galaxy wrapper id": "maf_stats", - "Galaxy tool ids": [ - "maf_stats1" - ], - "Description": "MAF Coverage statistics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "maf_stats", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats", - "Galaxy wrapper version": "1.0.2+galaxy0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "mageck", - "Galaxy tool ids": [ - "mageck_count", - "mageck_gsea", - "mageck_mle", - "mageck_pathway", - "mageck_test" - ], - "Description": "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.", - "bio.tool id": "mageck", - "bio.tool ids": [ - "mageck" - ], - "biii": null, - "bio.tool name": "MAGeCK", - "bio.tool description": "Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.", - "EDAM operation": [ - "Genetic variation analysis" - ], - "EDAM topic": [ - "Genetics", - "Genetic variation", - "Genomics" - ], - "Status": "To update", - "Source": "https://sourceforge.net/projects/mageck/", - "ToolShed categories": [ - "Genome editing" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck", - "Galaxy wrapper version": "0.5.9.2", - "Conda id": "mageck", - "Conda version": "0.5.9.5", - "EDAM operation (no superclasses)": [ - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Genetics", - "Genetic variation", - "Genomics" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "maker", - "Galaxy tool ids": [ - "maker", - "maker_map_ids" - ], - "Description": "MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.", - "bio.tool id": "maker", - "bio.tool ids": [ - "maker" - ], - "biii": null, - "bio.tool name": "MAKER", - "bio.tool description": "Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Genomics", - "DNA", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.yandell-lab.org/software/maker.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker", - "Galaxy wrapper version": "2.31.11", - "Conda id": "maker", - "Conda version": "3.01.03", - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "DNA", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "malt", - "Galaxy tool ids": [ - "malt_run" - ], - "Description": "Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/husonlab/malt", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "malt_run", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt", - "Galaxy wrapper version": "0.5.3", - "Conda id": "malt", - "Conda version": "0.62", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "map_param_value", - "Galaxy tool ids": [ - "map_param_value" - ], - "Description": "Map a parameter value to another value", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "map_param_value", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value", - "Galaxy wrapper version": "0.2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mapseq", - "Galaxy tool ids": [ - "mapseq" - ], - "Description": "fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.", - "bio.tool id": "mapseq", - "bio.tool ids": [ - "mapseq" - ], - "biii": null, - "bio.tool name": "MAPseq", - "bio.tool description": "Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .", - "EDAM operation": [ - "k-mer counting" - ], - "EDAM topic": [ - "Functional, regulatory and non-coding RNA", - "Sequence analysis", - "Sequence sites, features and motifs" - ], - "Status": "To update", - "Source": "https://github.com/jfmrod/MAPseq", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "mapseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq", - "Galaxy wrapper version": "2.1.1", - "Conda id": "perl", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Functional, regulatory and non-coding RNA", - "Sequence analysis", - "Sequence sites, features and motifs" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mash", - "Galaxy tool ids": [ - "mash_screen", - "mash_sketch" - ], - "Description": "Fast genome and metagenome distance estimation using MinHash", - "bio.tool id": "mash", - "bio.tool ids": [ - "mash" - ], - "biii": null, - "bio.tool name": "Mash", - "bio.tool description": "Fast genome and metagenome distance estimation using MinHash.", - "EDAM operation": [ - "Sequence distance matrix generation" - ], - "EDAM topic": [ - "Genomics", - "Metagenomics", - "Statistics and probability", - "Sequence analysis", - "DNA mutation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/Mash", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash", - "Galaxy wrapper version": "2.3", - "Conda id": "mash", - "Conda version": "2.3", - "EDAM operation (no superclasses)": [ - "Sequence distance matrix generation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Statistics and probability", - "Sequence analysis", - "DNA mutation" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "mashmap", - "Galaxy tool ids": [ - "mashmap" - ], - "Description": "Fast local alignment boundaries", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mashmap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap", - "Galaxy wrapper version": "3.1.3", - "Conda id": "mashmap", - "Conda version": "3.1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "masigpro", - "Galaxy tool ids": [ - "masigpro" - ], - "Description": "Identify significantly differential expression profiles in time-course microarray experiments", - "bio.tool id": "masigpro", - "bio.tool ids": [ - "masigpro" - ], - "biii": null, - "bio.tool name": "maSigPro", - "bio.tool description": "Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.", - "EDAM operation": [ - "Regression analysis" - ], - "EDAM topic": [ - "Gene expression", - "Molecular genetics", - "Microarray experiment", - "RNA-Seq" - ], - "Status": "To update", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "masigpro", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro", - "Galaxy wrapper version": "1.49.3", - "Conda id": "coreutils", - "Conda version": "8.25", - "EDAM operation (no superclasses)": [ - "Regression analysis" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "Microarray experiment", - "RNA-Seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "maxbin2", - "Galaxy tool ids": [ - "maxbin2" - ], - "Description": "clusters metagenomic contigs into bins", - "bio.tool id": "maxbin", - "bio.tool ids": [ - "maxbin" - ], - "biii": null, - "bio.tool name": "MaxBin", - "bio.tool description": "Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.", - "EDAM operation": [ - "Sequence assembly" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence assembly", - "Microbiology" - ], - "Status": "To update", - "Source": "https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "maxbin2", - "Galaxy wrapper owner": "mbernt", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2", - "Galaxy wrapper version": null, - "Conda id": "maxbin2", - "Conda version": "2.2.7", - "EDAM operation (no superclasses)": [ - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence assembly", - "Microbiology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "mcl", - "Galaxy tool ids": [ - "mcl" - ], - "Description": "The Markov Cluster Algorithm, a cluster algorithm for graphs", - "bio.tool id": "mcl", - "bio.tool ids": [ - "mcl" - ], - "biii": null, - "bio.tool name": "MCL", - "bio.tool description": "MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.", - "EDAM operation": [ - "Clustering", - "Network analysis", - "Gene regulatory network analysis" - ], - "EDAM topic": [ - "Molecular interactions, pathways and networks" - ], - "Status": "Up-to-date", - "Source": "https://micans.org/mcl/man/mcl.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mcl", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/mcl", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl", - "Galaxy wrapper version": "22.282", - "Conda id": "mcl", - "Conda version": "22.282", - "EDAM operation (no superclasses)": [ - "Clustering", - "Gene regulatory network analysis" - ], - "EDAM topic (no superclasses)": [ - "Molecular interactions, pathways and networks" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "medaka", - "Galaxy tool ids": [ - "medaka_consensus", - "medaka_consensus_pipeline", - "medaka_snp", - "medaka_variant" - ], - "Description": "Sequence correction provided by ONT Research", - "bio.tool id": "medaka", - "bio.tool ids": [ - "medaka" - ], - "biii": null, - "bio.tool name": "Medaka", - "bio.tool description": "medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.", - "EDAM operation": [ - "Base-calling", - "Variant calling", - "Sequence assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Machine learning" - ], - "Status": "To update", - "Source": "https://github.com/nanoporetech/medaka", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka", - "Galaxy wrapper version": "1.7.2", - "Conda id": "medaka", - "Conda version": "1.11.3", - "EDAM operation (no superclasses)": [ - "Base-calling", - "Variant calling", - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Machine learning" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "megahit", - "Galaxy tool ids": [ - "megahit" - ], - "Description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.", - "bio.tool id": "megahit", - "bio.tool ids": [ - "megahit" - ], - "biii": null, - "bio.tool name": "MEGAHIT", - "bio.tool description": "Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Metagenomics", - "Sequencing", - "Ecology", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/voutcn/megahit", - "ToolShed categories": [ - "Sequence Analysis", - "Assembly", - "Metagenomics" - ], - "ToolShed id": "megahit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit", - "Galaxy wrapper version": "1.2.9", - "Conda id": "megahit", - "Conda version": "1.2.9", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "megahit_contig2fastg", - "Galaxy tool ids": [ - "megahit_contig2fastg" - ], - "Description": "A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)", - "bio.tool id": "megahit", - "bio.tool ids": [ - "megahit" - ], - "biii": null, - "bio.tool name": "MEGAHIT", - "bio.tool description": "Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Metagenomics", - "Sequencing", - "Ecology", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp", - "ToolShed categories": [ - "Sequence Analysis", - "Assembly", - "Metagenomics" - ], - "ToolShed id": "megahit_contig2fastg", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg", - "Galaxy wrapper version": "1.1.3", - "Conda id": "megahit", - "Conda version": "1.2.9", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "megan", - "Galaxy tool ids": [ - "megan_blast2lca", - "megan_blast2rma", - "megan_daa2info", - "megan_daa2rma", - "megan_daa_meganizer", - "megan_read_extractor", - "megan_sam2rma" - ], - "Description": "MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).", - "bio.tool id": "megan", - "bio.tool ids": [ - "megan" - ], - "biii": null, - "bio.tool name": "MEGAN", - "bio.tool description": "Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.", - "EDAM operation": [ - "Sequence analysis", - "Taxonomic classification" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/husonlab/megan-ce", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "megan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan", - "Galaxy wrapper version": "6.21.7", - "Conda id": "megan", - "Conda version": "6.25.9", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "meme", - "Galaxy tool ids": [ - "meme_dreme", - "meme_fimo", - "meme_meme", - "meme_psp_gen" - ], - "Description": "The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.", - "bio.tool id": "meme_meme", - "bio.tool ids": [ - "meme_meme", - "meme_fimo" - ], - "biii": null, - "bio.tool name": "meme_meme", - "bio.tool description": "An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.", - "EDAM operation": [ - "Nucleic acid feature detection", - "Protein feature detection", - "Statistical calculation" - ], - "EDAM topic": [ - "Data mining", - "Sequence analysis", - "Genetic variation", - "Statistics and probability" - ], - "Status": "To update", - "Source": "http://meme-suite.org/", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "meme", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme", - "Galaxy wrapper version": "5.4.1", - "Conda id": "meme", - "Conda version": "5.5.5", - "EDAM operation (no superclasses)": [ - "Nucleic acid feature detection", - "Protein feature detection", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Data mining", - "Sequence analysis", - "Genetic variation", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "meme_chip", - "Galaxy tool ids": [ - "meme_chip" - ], - "Description": "Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://meme-suite.org/", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "meme_chip", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip", - "Galaxy wrapper version": "4.11.2", - "Conda id": "graphicsmagick", - "Conda version": "1.3.26", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "meningotype", - "Galaxy tool ids": [ - "meningotype" - ], - "Description": "Assign sequence type to N. meningitidis genome assemblies", - "bio.tool id": "meningotype", - "bio.tool ids": [ - "meningotype" - ], - "biii": null, - "bio.tool name": "meningotype", - "bio.tool description": "In silico typing of Neisseria meningitidis contigs.", - "EDAM operation": [ - "Genotyping", - "Multilocus sequence typing" - ], - "EDAM topic": [ - "Microbiology", - "Genotype and phenotype" - ], - "Status": "Up-to-date", - "Source": "https://github.com/MDU-PHL/meningotype", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "meningotype", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype", - "Galaxy wrapper version": "0.8.5", - "Conda id": "meningotype", - "Conda version": "0.8.5", - "EDAM operation (no superclasses)": [ - "Multilocus sequence typing" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Genotype and phenotype" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "merlin", - "Galaxy tool ids": [ - "merlin" - ], - "Description": "Pedigree Analysis package", - "bio.tool id": "merlin", - "bio.tool ids": [ - "merlin" - ], - "biii": null, - "bio.tool name": "Merlin", - "bio.tool description": "Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation", - "EDAM operation": [ - "Haplotype mapping", - "Genetic mapping" - ], - "EDAM topic": [ - "GWAS study", - "Mapping" - ], - "Status": "Up-to-date", - "Source": "http://csg.sph.umich.edu/abecasis/Merlin/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "merlin", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin", - "Galaxy wrapper version": "1.1.2", - "Conda id": "merlin", - "Conda version": "1.1.2", - "EDAM operation (no superclasses)": [ - "Haplotype mapping" - ], - "EDAM topic (no superclasses)": [ - "GWAS study", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "merqury", - "Galaxy tool ids": [ - "merqury", - "merquryplot" - ], - "Description": "Merqury is a tool for evaluating genomes assemblies based of k-mer operations.", - "bio.tool id": "merqury", - "bio.tool ids": [ - "merqury" - ], - "biii": null, - "bio.tool name": "Merqury", - "bio.tool description": "Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.", - "EDAM operation": [ - "Genome assembly", - "k-mer counting", - "Scaffolding", - "Phasing", - "De-novo assembly" - ], - "EDAM topic": [ - "Sequence assembly", - "Whole genome sequencing", - "Plant biology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/merqury", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "merqury", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury", - "Galaxy wrapper version": "1.3", - "Conda id": "merqury", - "Conda version": "1.3", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "k-mer counting", - "Scaffolding", - "Phasing", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Whole genome sequencing", - "Plant biology" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "meryl", - "Galaxy tool ids": [ - "meryl_arithmetic_kmers", - "meryl_count_kmers", - "meryl_filter_kmers", - "meryl_groups_kmers", - "meryl_histogram_kmers", - "meryl_print", - "meryl_trio_mode" - ], - "Description": "Meryl a k-mer counter.", - "bio.tool id": "meryl", - "bio.tool ids": [ - "meryl" - ], - "biii": null, - "bio.tool name": "Meryl", - "bio.tool description": "Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.", - "EDAM operation": [ - "k-mer counting" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Genomics", - "Sequence analysis", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/meryl", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "meryl", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl", - "Galaxy wrapper version": "1.3", - "Conda id": "merqury", - "Conda version": "1.3", - "EDAM operation (no superclasses)": [ - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Genomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metabat2", - "Galaxy tool ids": [ - "metabat2_jgi_summarize_bam_contig_depths", - "metabat2" - ], - "Description": "MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.", - "bio.tool id": "MetaBAT_2", - "bio.tool ids": [ - "MetaBAT_2" - ], - "biii": null, - "bio.tool name": "MetaBAT 2", - "bio.tool description": "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different \"bins\", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning", - "EDAM operation": [ - "Read binning", - "Sequence assembly", - "Genome annotation" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence assembly", - "Metagenomic sequencing" - ], - "Status": "Up-to-date", - "Source": "https://bitbucket.org/berkeleylab/metabat/src/master/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "metabat2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2", - "Galaxy wrapper version": "2.15", - "Conda id": "metabat2", - "Conda version": "2.15", - "EDAM operation (no superclasses)": [ - "Read binning", - "Sequence assembly", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence assembly", - "Metagenomic sequencing" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "metabuli", - "Galaxy tool ids": [ - "metabuli_classify" - ], - "Description": "Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences", - "bio.tool id": "metabuli", - "bio.tool ids": [ - "metabuli" - ], - "biii": null, - "bio.tool name": "metabuli", - "bio.tool description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", - "EDAM operation": [ - "Taxonomic classification" - ], - "EDAM topic": [ - "Taxonomy" - ], - "Status": "Up-to-date", - "Source": "https://github.com/steineggerlab/Metabuli", - "ToolShed categories": [ - "Sequence Analysis", - "Metagenomics" - ], - "ToolShed id": "metabuli", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli", - "Galaxy wrapper version": "1.0.5", - "Conda id": "metabuli", - "Conda version": "1.0.5", - "EDAM operation (no superclasses)": [ - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metaeuk", - "Galaxy tool ids": [ - "metaeuk_easy_predict" - ], - "Description": "MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. ", - "bio.tool id": "MetaEuk", - "bio.tool ids": [ - "MetaEuk" - ], - "biii": null, - "bio.tool name": "MetaEuk", - "bio.tool description": "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics", - "EDAM operation": [ - "Homology-based gene prediction" - ], - "EDAM topic": [ - "Metagenomics", - "Gene and protein families" - ], - "Status": "To update", - "Source": "https://github.com/soedinglab/metaeuk", - "ToolShed categories": [ - "Sequence Analysis", - "Genome annotation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk", - "Galaxy wrapper version": "5.34c21f2", - "Conda id": "metaeuk", - "Conda version": "6.a5d39d9", - "EDAM operation (no superclasses)": [ - "Homology-based gene prediction" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Gene and protein families" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metagenomeseq", - "Galaxy tool ids": [ - "metagenomeseq_normalizaton" - ], - "Description": "metagenomeSeq Normalization", - "bio.tool id": "metagenomeseq", - "bio.tool ids": [ - "metagenomeseq" - ], - "biii": null, - "bio.tool name": "metagenomeSeq", - "bio.tool description": "Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.", - "EDAM operation": [ - "Sequence visualisation", - "Statistical calculation" - ], - "EDAM topic": [ - "Metagenomics", - "Sequencing" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "metagenomeseq_normalization", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq", - "Galaxy wrapper version": "1.16.0-0.0.1", - "Conda id": "bioconductor-metagenomeseq", - "Conda version": "1.43.0", - "EDAM operation (no superclasses)": [ - "Sequence visualisation", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "metaphlan", - "Galaxy tool ids": [ - "customize_metaphlan_database", - "extract_metaphlan_database", - "merge_metaphlan_tables", - "metaphlan" - ], - "Description": "MetaPhlAn for Metagenomic Phylogenetic Analysis", - "bio.tool id": "metaphlan", - "bio.tool ids": [ - "metaphlan" - ], - "biii": null, - "bio.tool name": "MetaPhlAn", - "bio.tool description": "Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", - "EDAM operation": [ - "Nucleic acid sequence analysis", - "Phylogenetic tree analysis" - ], - "EDAM topic": [ - "Metagenomics", - "Phylogenomics" - ], - "Status": "To update", - "Source": "https://github.com/biobakery/MetaPhlAn", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "metaphlan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan", - "Galaxy wrapper version": "4.0.6", - "Conda id": "metaphlan", - "Conda version": "4.1.1", - "EDAM operation (no superclasses)": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Phylogenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "metawrapmg", - "Galaxy tool ids": [ - "metawrapmg_binning" - ], - "Description": "A flexible pipeline for genome-resolved metagenomic data analysis", - "bio.tool id": "metawrap", - "bio.tool ids": [ - "metawrap" - ], - "biii": null, - "bio.tool name": "MetaWRAP", - "bio.tool description": "MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.", - "EDAM operation": [ - "Read binning", - "Sequence assembly", - "Genome annotation", - "Sequence trimming", - "Demultiplexing" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Metagenomic sequencing", - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/bxlab/metaWRAP", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "metawrapmg_binning", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg", - "Galaxy wrapper version": "1.3.0", - "Conda id": "metawrap-mg", - "Conda version": "1.3.0", - "EDAM operation (no superclasses)": [ - "Read binning", - "Sequence assembly", - "Genome annotation", - "Sequence trimming", - "Demultiplexing" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Metagenomic sequencing", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "migmap", - "Galaxy tool ids": [ - "migmap" - ], - "Description": "mapper for full-length T- and B-cell repertoire sequencing", - "bio.tool id": "MiGMAP", - "bio.tool ids": [ - "MiGMAP" - ], - "biii": null, - "bio.tool name": "MiGMAP", - "bio.tool description": "Mapper for full-length T- and B-cell repertoire sequencing.", - "EDAM operation": [ - "Sequence analysis", - "Read mapping" - ], - "EDAM topic": [ - "Immunoproteins, genes and antigens", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/mikessh/migmap", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "migmap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap", - "Galaxy wrapper version": "1.0.3", - "Conda id": "migmap", - "Conda version": "1.0.3", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "minia", - "Galaxy tool ids": [ - "minia" - ], - "Description": "Short-read assembler based on a de Bruijn graph", - "bio.tool id": "minia", - "bio.tool ids": [ - "minia" - ], - "biii": null, - "bio.tool name": "Minia", - "bio.tool description": "Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://gatb.inria.fr/software/minia/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "minia", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia", - "Galaxy wrapper version": "3.2.6", - "Conda id": "minia", - "Conda version": "3.2.6", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "miniasm", - "Galaxy tool ids": [ - "miniasm" - ], - "Description": "Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)", - "bio.tool id": "miniasm", - "bio.tool ids": [ - "miniasm" - ], - "biii": null, - "bio.tool name": "miniasm", - "bio.tool description": "Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.", - "EDAM operation": [ - "De-novo assembly" - ], - "EDAM topic": [ - "Genomics", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/lh3/miniasm", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "miniasm", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm", - "Galaxy wrapper version": "0.3_r179", - "Conda id": "miniasm", - "Conda version": "0.3", - "EDAM operation (no superclasses)": [ - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "minimap2", - "Galaxy tool ids": [ - "minimap2" - ], - "Description": "A fast pairwise aligner for genomic and spliced nucleotide sequences", - "bio.tool id": "minimap2", - "bio.tool ids": [ - "minimap2" - ], - "biii": null, - "bio.tool name": "Minimap2", - "bio.tool description": "Pairwise aligner for genomic and spliced nucleotide sequences", - "EDAM operation": [ - "Pairwise sequence alignment" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/lh3/minimap2", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "minimap2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2", - "Galaxy wrapper version": "2.28", - "Conda id": "minimap2", - "Conda version": "2.28", - "EDAM operation (no superclasses)": [ - "Pairwise sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "miniprot", - "Galaxy tool ids": [ - "miniprot", - "miniprot_index" - ], - "Description": "Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.", - "bio.tool id": "miniprot", - "bio.tool ids": [ - "miniprot" - ], - "biii": null, - "bio.tool name": "miniprot", - "bio.tool description": "Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.", - "EDAM operation": [ - "Sequence alignment", - "Protein sequence analysis" - ], - "EDAM topic": [ - "Sequence sites, features and motifs", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/lh3/miniprot", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot", - "Galaxy wrapper version": "0.13", - "Conda id": "miniprot", - "Conda version": "0.13", - "EDAM operation (no superclasses)": [ - "Sequence alignment", - "Protein sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence sites, features and motifs", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "mirmachine", - "Galaxy tool ids": [ - "mirmachine" - ], - "Description": "Tool to detect miRNA in genome sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/sinanugur/MirMachine", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mirmachine", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine", - "Galaxy wrapper version": "0.2.13", - "Conda id": "mirmachine", - "Conda version": "0.2.13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mirnature", - "Galaxy tool ids": [ - "mirnature" - ], - "Description": "Computational detection of canonical microRNAs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/Bierinformatik/miRNAture", - "ToolShed categories": [ - "RNA", - "Sequence Analysis" - ], - "ToolShed id": "mirnature", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/Bierinformatik/miRNAture", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature", - "Galaxy wrapper version": "1.1", - "Conda id": "mirnature", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mitobim", - "Galaxy tool ids": [ - "mitobim" - ], - "Description": "assemble mitochondrial genomes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/chrishah/MITObim", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "mitobim", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim", - "Galaxy wrapper version": "1.9.1", - "Conda id": "mitobim", - "Conda version": "1.9.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mitos", - "Galaxy tool ids": [ - "mitos", - "mitos2" - ], - "Description": "de-novo annotation of metazoan mitochondrial genomes", - "bio.tool id": "mitos", - "bio.tool ids": [ - "mitos" - ], - "biii": null, - "bio.tool name": "MITOS", - "bio.tool description": "De novo metazoan mitochondrial genome annotation.", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Zoology", - "Whole genome sequencing" - ], - "Status": "To update", - "Source": "http://mitos.bioinf.uni-leipzig.de/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mitos", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos", - "Galaxy wrapper version": "1.1.7", - "Conda id": "mitos", - "Conda version": "2.1.9", - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Zoology", - "Whole genome sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mlst", - "Galaxy tool ids": [ - "mlst", - "mlst_list" - ], - "Description": "Scan contig files against PubMLST typing schemes", - "bio.tool id": "mlst", - "bio.tool ids": [ - "mlst" - ], - "biii": null, - "bio.tool name": "MLST", - "bio.tool description": "Multi Locus Sequence Typing from an assembled genome or from a set of reads.", - "EDAM operation": [ - "Multilocus sequence typing" - ], - "EDAM topic": [ - "Immunoproteins and antigens" - ], - "Status": "To update", - "Source": "https://github.com/tseemann/mlst", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mlst", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst", - "Galaxy wrapper version": "2.22.0", - "Conda id": "mlst", - "Conda version": "2.23.0", - "EDAM operation (no superclasses)": [ - "Multilocus sequence typing" - ], - "EDAM topic (no superclasses)": [ - "Immunoproteins and antigens" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "moabs", - "Galaxy tool ids": [ - "moabs" - ], - "Description": "MOABS for differential methylation analysis on Bisulfite sequencing data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/sunnyisgalaxy/moabs", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "moabs", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/sunnyisgalaxy/moabs", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs", - "Galaxy wrapper version": "1.3.4.6", - "Conda id": "moabs", - "Conda version": "1.3.9.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mosdepth", - "Galaxy tool ids": [ - "mosdepth" - ], - "Description": "fast and flexible BAM/CRAM depth calculation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/brentp/mosdepth", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "mosdepth", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth", - "Galaxy wrapper version": "0.3.8", - "Conda id": "mosdepth", - "Conda version": "0.3.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mothur", - "Galaxy tool ids": [ - "mothur_align_check", - "mothur_align_seqs", - "mothur_amova", - "mothur_anosim", - "mothur_bin_seqs", - "mothur_biom_info", - "mothur_chimera_bellerophon", - "mothur_chimera_ccode", - "mothur_chimera_check", - "mothur_chimera_perseus", - "mothur_chimera_pintail", - "mothur_chimera_slayer", - "mothur_chimera_uchime", - "mothur_chimera_vsearch", - "mothur_chop_seqs", - "mothur_classify_otu", - "mothur_classify_seqs", - "mothur_classify_tree", - "mothur_clearcut", - "mothur_cluster_classic", - "mothur_cluster_fragments", - "mothur_cluster_split", - "mothur_cluster", - "mothur_collect_shared", - "mothur_collect_single", - "mothur_consensus_seqs", - "mothur_cooccurrence", - "mothur_corr_axes", - "mothur_count_groups", - "mothur_count_seqs", - "mothur_create_database", - "mothur_degap_seqs", - "mothur_deunique_seqs", - "mothur_deunique_tree", - "mothur_dist_seqs", - "mothur_dist_shared", - "mothur_fastq_info", - "mothur_filter_seqs", - "mothur_filter_shared", - "mothur_get_communitytype", - "mothur_get_coremicrobiome", - "mothur_get_dists", - "mothur_get_group", - "mothur_get_groups", - "mothur_get_label", - "mothur_get_lineage", - "mothur_get_mimarkspackage", - "mothur_get_otulabels", - "mothur_get_otulist", - "mothur_get_oturep", - "mothur_get_otus", - "mothur_get_rabund", - "mothur_get_relabund", - "mothur_get_sabund", - "mothur_get_seqs", - "mothur_get_sharedseqs", - "mothur_heatmap_bin", - "mothur_heatmap_sim", - "mothur_homova", - "mothur_indicator", - "mothur_lefse", - "mothur_libshuff", - "mothur_list_otulabels", - "mothur_list_seqs", - "mothur_make_biom", - "mothur_make_contigs", - "mothur_make_design", - "mothur_make_fastq", - "mothur_make_group", - "mothur_make_lefse", - "mothur_make_lookup", - "mothur_make_shared", - "mothur_make_sra", - "mothur_mantel", - "mothur_merge_count", - "mothur_merge_files", - "mothur_merge_groups", - "mothur_merge_sfffiles", - "mothur_merge_taxsummary", - "mothur_metastats", - "mothur_mimarks_attributes", - "mothur_nmds", - "mothur_normalize_shared", - "mothur_otu_association", - "mothur_otu_hierarchy", - "mothur_pairwise_seqs", - "mothur_parse_list", - "mothur_parsimony", - "mothur_pca", - "mothur_pcoa", - "mothur_pcr_seqs", - "mothur_phylo_diversity", - "mothur_phylotype", - "mothur_pre_cluster", - "mothur_primer_design", - "mothur_rarefaction_shared", - "mothur_rarefaction_single", - "mothur_remove_dists", - "mothur_remove_groups", - "mothur_remove_lineage", - "mothur_remove_otulabels", - "mothur_remove_otus", - "mothur_remove_rare", - "mothur_remove_seqs", - "mothur_rename_seqs", - "mothur_reverse_seqs", - "mothur_screen_seqs", - "mothur_sens_spec", - "mothur_seq_error", - "mothur_sffinfo", - "mothur_shhh_flows", - "mothur_shhh_seqs", - "mothur_sort_seqs", - "mothur_split_abund", - "mothur_split_groups", - "mothur_sub_sample", - "mothur_summary_qual", - "mothur_summary_seqs", - "mothur_summary_shared", - "mothur_summary_single", - "mothur_summary_tax", - "mothur_taxonomy_to_krona", - "mothur_tree_shared", - "mothur_trim_flows", - "mothur_trim_seqs", - "mothur_unifrac_unweighted", - "mothur_unifrac_weighted", - "mothur_unique_seqs", - "mothur_venn" - ], - "Description": "Mothur wrappers", - "bio.tool id": "mothur", - "bio.tool ids": [ - "mothur" - ], - "biii": null, - "bio.tool name": "mothur", - "bio.tool description": "Open-source, platform-independent, community-supported software for describing and comparing microbial communities", - "EDAM operation": [ - "DNA barcoding", - "Sequencing quality control", - "Sequence clustering", - "Taxonomic classification", - "Visualisation", - "Sequence read processing", - "Phylogenetic analysis" - ], - "EDAM topic": [ - "Microbial ecology", - "Taxonomy", - "Sequence analysis", - "Phylogeny" - ], - "Status": "To update", - "Source": "https://www.mothur.org", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "mothur", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur", - "Galaxy wrapper version": "1.0", - "Conda id": "mothur", - "Conda version": "1.48.0", - "EDAM operation (no superclasses)": [ - "DNA barcoding", - "Sequencing quality control", - "Sequence clustering", - "Taxonomic classification", - "Visualisation", - "Sequence read processing", - "Phylogenetic analysis" - ], - "EDAM topic (no superclasses)": [ - "Microbial ecology", - "Taxonomy", - "Sequence analysis", - "Phylogeny" - ], - "Available on UseGalaxy.org": 129, - "Available on UseGalaxy.org.au": 129, - "Available on UseGalaxy.eu": 129, - "Available on UseGalaxy.org.fr": 129 - }, - { - "Galaxy wrapper id": "msaboot", - "Galaxy tool ids": [ - "msaboot" - ], - "Description": "A multiple sequences alignment bootstrapping tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/phac-nml/msaboot", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "msaboot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot", - "Galaxy wrapper version": "0.1.2", - "Conda id": "msaboot", - "Conda version": "0.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "multigps", - "Galaxy tool ids": [ - "multigps" - ], - "Description": "Analyzes collections of multi-condition ChIP-seq data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://mahonylab.org/software/multigps/", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "multigps", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps", - "Galaxy wrapper version": "0.74.0", - "Conda id": "fonts-conda-ecosystem", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "multigsea", - "Galaxy tool ids": [ - "multigsea" - ], - "Description": "GSEA-based pathway enrichment analysis for multi-omics data", - "bio.tool id": "multiGSEA", - "bio.tool ids": [ - "multiGSEA" - ], - "biii": null, - "bio.tool name": "multiGSEA", - "bio.tool description": "A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.", - "EDAM operation": [ - "Gene-set enrichment analysis", - "Aggregation", - "Pathway analysis" - ], - "EDAM topic": [ - "Metabolomics", - "Molecular interactions, pathways and networks", - "Proteomics", - "Transcriptomics", - "Small molecules" - ], - "Status": "Up-to-date", - "Source": "https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html", - "ToolShed categories": [ - "Transcriptomics", - "Proteomics", - "Statistics" - ], - "ToolShed id": "multigsea", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea", - "Galaxy wrapper version": "1.12.0", - "Conda id": "bioconductor-multigsea", - "Conda version": "1.12.0", - "EDAM operation (no superclasses)": [ - "Gene-set enrichment analysis", - "Aggregation", - "Pathway analysis" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics", - "Molecular interactions, pathways and networks", - "Proteomics", - "Transcriptomics", - "Small molecules" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "multiqc", - "Galaxy tool ids": [ - "multiqc" - ], - "Description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report", - "bio.tool id": "multiqc", - "bio.tool ids": [ - "multiqc" - ], - "biii": null, - "bio.tool name": "MultiQC", - "bio.tool description": "MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.", - "EDAM operation": [ - "Validation", - "Sequencing quality control" - ], - "EDAM topic": [ - "Sequencing", - "Bioinformatics", - "Sequence analysis", - "Genomics" - ], - "Status": "To update", - "Source": "http://multiqc.info/", - "ToolShed categories": [ - "Fastq Manipulation", - "Statistics", - "Visualization" - ], - "ToolShed id": "multiqc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc", - "Galaxy wrapper version": "1.11", - "Conda id": "multiqc", - "Conda version": "1.22.2", - "EDAM operation (no superclasses)": [ - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Bioinformatics", - "Sequence analysis", - "Genomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "mummer4", - "Galaxy tool ids": [ - "mummer_delta_filter", - "mummer_dnadiff", - "mummer_mummer", - "mummer_mummerplot", - "mummer_nucmer", - "mummer_show_coords" - ], - "Description": "Mummer4 Tools", - "bio.tool id": "mummer4", - "bio.tool ids": [ - "mummer4" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/mummer4/mummer", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mummer4", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4", - "Galaxy wrapper version": "4.0.0rc1", - "Conda id": "mummer4", - "Conda version": "4.0.0rc1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "mykrobe", - "Galaxy tool ids": [ - "mykrobe_predict" - ], - "Description": "Antibiotic resistance predictions", - "bio.tool id": "Mykrobe", - "bio.tool ids": [ - "Mykrobe" - ], - "biii": null, - "bio.tool name": "Mykrobe", - "bio.tool description": "Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed", - "EDAM operation": [ - "Antimicrobial resistance prediction", - "Variant calling", - "Genotyping", - "Sequence trimming" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Genotype and phenotype", - "Probes and primers", - "Genetic variation", - "Metagenomics" - ], - "Status": "To update", - "Source": "https://github.com/Mykrobe-tools/mykrobe", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "mykrobe", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe", - "Galaxy wrapper version": "0.10.0", - "Conda id": "mykrobe", - "Conda version": "0.13.0", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction", - "Variant calling", - "Genotyping", - "Sequence trimming" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Genotype and phenotype", - "Probes and primers", - "Genetic variation", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mzmine", - "Galaxy tool ids": [ - "mzmine_batch" - ], - "Description": "mass-spectrometry data processing, with the main focus on LC-MS data", - "bio.tool id": "mzmine", - "bio.tool ids": [ - "mzmine" - ], - "biii": null, - "bio.tool name": "MZmine", - "bio.tool description": "Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.", - "EDAM operation": [ - "Natural product identification", - "Standardisation and normalisation", - "Peptide database search", - "Deisotoping", - "Clustering", - "Filtering", - "Chromatographic alignment", - "Peak detection", - "Peptide identification", - "Chromatogram visualisation", - "Mass spectrum visualisation", - "Structure visualisation", - "Plotting", - "Heat map generation" - ], - "EDAM topic": [ - "Proteomics", - "Metabolomics", - "Proteomics experiment", - "Small molecules" - ], - "Status": "Up-to-date", - "Source": "http://mzmine.github.io/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "mzmine_batch", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine", - "Galaxy wrapper version": "3.9.0", - "Conda id": "mzmine", - "Conda version": "3.9.0", - "EDAM operation (no superclasses)": [ - "Natural product identification", - "Standardisation and normalisation", - "Peptide database search", - "Deisotoping", - "Clustering", - "Filtering", - "Chromatographic alignment", - "Peak detection", - "Peptide identification", - "Chromatogram visualisation", - "Mass spectrum visualisation", - "Structure visualisation", - "Plotting", - "Heat map generation" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Metabolomics", - "Proteomics experiment", - "Small molecules" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "naltorfs", - "Galaxy tool ids": [ - "bicodon_counts_from_fasta", - "codon_freq_from_bicodons", - "find_nested_alt_orfs" - ], - "Description": "nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/BlankenbergLab/nAltORFs", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs", - "Galaxy wrapper version": "0.1.2", - "Conda id": "naltorfs", - "Conda version": "0.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nanocompore", - "Galaxy tool ids": [ - "nanocompore_db", - "nanocompore_sampcomp" - ], - "Description": "Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.", - "bio.tool id": "Nanocompore", - "bio.tool ids": [ - "Nanocompore" - ], - "biii": null, - "bio.tool name": "Nanocompore", - "bio.tool description": "RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro", - "EDAM operation": [ - "Post-translation modification site prediction", - "PolyA signal detection", - "Genotyping", - "k-mer counting" - ], - "EDAM topic": [ - "Functional, regulatory and non-coding RNA", - "RNA-Seq", - "Gene transcripts", - "Transcriptomics", - "Transcription factors and regulatory sites" - ], - "Status": "To update", - "Source": "https://nanocompore.rna.rocks/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "nanocompore", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore", - "Galaxy wrapper version": "1.0.0rc3.post2", - "Conda id": "nanocompore", - "Conda version": "1.0.4", - "EDAM operation (no superclasses)": [ - "PolyA signal detection", - "Genotyping", - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Functional, regulatory and non-coding RNA", - "RNA-Seq", - "Gene transcripts", - "Transcriptomics", - "Transcription factors and regulatory sites" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "nanoplot", - "Galaxy tool ids": [ - "nanoplot" - ], - "Description": "Plotting tool for long read sequencing data and alignments", - "bio.tool id": "nanoplot", - "bio.tool ids": [ - "nanoplot" - ], - "biii": null, - "bio.tool name": "NanoPlot", - "bio.tool description": "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences", - "EDAM operation": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" - ], - "EDAM topic": [ - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/wdecoster/NanoPlot", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "nanoplot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot", - "Galaxy wrapper version": "1.42.0", - "Conda id": "nanoplot", - "Conda version": "1.42.0", - "EDAM operation (no superclasses)": [ - "Scatter plot plotting", - "Box-Whisker plot plotting" - ], - "EDAM topic (no superclasses)": [ - "Genomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nanopolishcomp", - "Galaxy tool ids": [ - "nanopolishcomp_eventaligncollapse", - "nanopolishcomp_freqmethcalculate" - ], - "Description": "NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.", - "bio.tool id": "nanopolishcomp", - "bio.tool ids": [ - "nanopolishcomp" - ], - "biii": null, - "bio.tool name": "NanopolishComp", - "bio.tool description": "NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.", - "EDAM operation": [ - "Methylation analysis", - "Collapsing methods" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequencing", - "Genetic variation" - ], - "Status": "To update", - "Source": "https://a-slide.github.io/NanopolishComp", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "nanopolishcomp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp", - "Galaxy wrapper version": "0.6.11", - "Conda id": "nanopolishcomp", - "Conda version": "0.6.12", - "EDAM operation (no superclasses)": [ - "Methylation analysis", - "Collapsing methods" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Sequencing", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "ncbi_acc_download", - "Galaxy tool ids": [ - "ncbi_acc_download" - ], - "Description": "Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/kblin/ncbi-acc-download", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "ncbi_acc_download", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download", - "Galaxy wrapper version": "0.2.8", - "Conda id": "ncbi-acc-download", - "Conda version": "0.2.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ncbi_datasets", - "Galaxy tool ids": [ - "datasets_download_gene", - "datasets_download_genome" - ], - "Description": "NCBI datasets downloads biological sequence data across all domains of life from NCBI.", - "bio.tool id": "ncbi_datasets", - "bio.tool ids": [ - "ncbi_datasets" - ], - "biii": null, - "bio.tool name": "NCBI Datasets", - "bio.tool description": "NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.", - "EDAM operation": [ - "Data handling", - "Sequence database search", - "Data retrieval" - ], - "EDAM topic": [ - "Biological databases" - ], - "Status": "To update", - "Source": "https://github.com/ncbi/datasets", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "ncbi_datasets", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets", - "Galaxy wrapper version": "16.6.0", - "Conda id": "ncbi-datasets-cli", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Data handling", - "Sequence database search", - "Data retrieval" - ], - "EDAM topic (no superclasses)": [ - "Biological databases" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "ncbi_entrez_direct", - "Galaxy tool ids": [ - "ncbi_entrez_direct_efetch", - "ncbi_entrez_direct_einfo", - "ncbi_entrez_direct_esearch" - ], - "Description": "NCBI Entrez Direct allow fetching data from NCBI Databases", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://www.ncbi.nlm.nih.gov/books/NBK179288/", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "ncbi_entrez_direct", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct", - "Galaxy wrapper version": "21.6", - "Conda id": "entrez-direct", - "Conda version": "21.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ncbi_entrez_eutils", - "Galaxy tool ids": [ - "ncbi_eutils_ecitmatch", - "ncbi_eutils_efetch", - "ncbi_eutils_egquery", - "ncbi_eutils_einfo", - "ncbi_eutils_elink", - "ncbi_eutils_epost", - "ncbi_eutils_esearch", - "ncbi_eutils_esummary" - ], - "Description": "NCBI Entrez E-Utilties allow fetching data from NCBI Databases", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "ncbi_entrez_eutils", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils", - "Galaxy wrapper version": "1.70", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ncbi_fcs_gx", - "Galaxy tool ids": [ - "ncbi_fcs_gx" - ], - "Description": "FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).", - "bio.tool id": "ncbi_fcs", - "bio.tool ids": [ - "ncbi_fcs" - ], - "biii": null, - "bio.tool name": "NCBI fcs", - "bio.tool description": "The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.", - "EDAM operation": [ - "Sequence assembly validation", - "Sequence trimming", - "Sequence contamination filtering" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/ncbi/fcs-gx", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ncbi_fcs_gx", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", - "Galaxy wrapper version": "0.5.0", - "Conda id": "ncbi-fcs-gx", - "Conda version": "0.5.0", - "EDAM operation (no superclasses)": [ - "Sequence assembly validation", - "Sequence trimming", - "Sequence contamination filtering" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "necat", - "Galaxy tool ids": [ - "necat" - ], - "Description": "Error correction and de-novo assembly for ONT Nanopore reads", - "bio.tool id": "necat", - "bio.tool ids": [ - "necat" - ], - "biii": null, - "bio.tool name": "NECAT", - "bio.tool description": "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.", - "EDAM operation": [ - "De-novo assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/xiaochuanle/NECAT", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "necat", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat", - "Galaxy wrapper version": "0.0.1_update20200803", - "Conda id": "necat", - "Conda version": "0.0.1_update20200803", - "EDAM operation (no superclasses)": [ - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "newick_utils", - "Galaxy tool ids": [ - "newick_display" - ], - "Description": "Perform operations on Newick trees", - "bio.tool id": "newick_utilities", - "bio.tool ids": [ - "newick_utilities" - ], - "biii": null, - "bio.tool name": "Newick Utilities", - "bio.tool description": "The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.", - "EDAM operation": [ - "Phylogenetic tree generation", - "Phylogenetic tree analysis", - "Phylogenetic tree reconstruction" - ], - "EDAM topic": [ - "Phylogeny", - "Genomics", - "Computer science" - ], - "Status": "To update", - "Source": "http://cegg.unige.ch/newick_utils", - "ToolShed categories": [ - "Visualization", - "Metagenomics" - ], - "ToolShed id": "newick_utils", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/tjunier/newick_utils", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils", - "Galaxy wrapper version": "1.6+galaxy1", - "Conda id": "newick_utils", - "Conda version": "1.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Phylogeny", - "Genomics", - "Computer science" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nextclade", - "Galaxy tool ids": [ - "nextalign", - "nextclade" - ], - "Description": "Identify differences between your sequences and a reference sequence used by Nextstrain", - "bio.tool id": "nextclade", - "bio.tool ids": [ - "nextclade" - ], - "biii": null, - "bio.tool name": "Nextclade", - "bio.tool description": "Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.", - "EDAM operation": [ - "Methylation analysis", - "Variant calling" - ], - "EDAM topic": [ - "Genomics", - "Sequence analysis", - "Cladistics" - ], - "Status": "To update", - "Source": "https://github.com/nextstrain/nextclade", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade", - "Galaxy wrapper version": "2.7.0", - "Conda id": "nextalign", - "Conda version": "2.14.0", - "EDAM operation (no superclasses)": [ - "Methylation analysis", - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Cladistics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "ngmlr", - "Galaxy tool ids": [ - "ngmlr" - ], - "Description": "CoNvex Gap-cost alignMents for Long Reads", - "bio.tool id": "ngmlr", - "bio.tool ids": [ - "ngmlr" - ], - "biii": null, - "bio.tool name": "NGMLR", - "bio.tool description": "An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.", - "EDAM operation": [ - "DNA mapping", - "Sequence alignment", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Sequencing", - "Mapping", - "DNA structural variation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/philres/ngmlr", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "ngmlr", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr", - "Galaxy wrapper version": "0.2.7", - "Conda id": "ngmlr", - "Conda version": "0.2.7", - "EDAM operation (no superclasses)": [ - "DNA mapping", - "Sequence alignment", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ngsutils", - "Galaxy tool ids": [ - "ngsutils_bam_filter" - ], - "Description": "NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.", - "bio.tool id": "ngsutils", - "bio.tool ids": [ - "ngsutils" - ], - "biii": null, - "bio.tool name": "NGSUtils", - "bio.tool description": "NGSUtils is a suite of software tools for working with next-generation sequencing datasets", - "EDAM operation": [ - "Read pre-processing", - "Sequencing quality control", - "Variant calling", - "Formatting", - "Sequence contamination filtering" - ], - "EDAM topic": [ - "Genomics", - "Transcriptomics" - ], - "Status": "To update", - "Source": "https://github.com/ngsutils/ngsutils", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils", - "Galaxy wrapper version": null, - "Conda id": "ngsutils", - "Conda version": "0.5.9", - "EDAM operation (no superclasses)": [ - "Read pre-processing", - "Variant calling", - "Formatting", - "Sequence contamination filtering" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nonpareil", - "Galaxy tool ids": [ - "nonpareil" - ], - "Description": "Estimate average coverage in metagenomic datasets", - "bio.tool id": "nonpareil", - "bio.tool ids": [ - "nonpareil" - ], - "biii": null, - "bio.tool name": "nonpareil", - "bio.tool description": "Estimate metagenomic coverage and sequence diversity", - "EDAM operation": [ - "Operation" - ], - "EDAM topic": [], - "Status": "To update", - "Source": "http://nonpareil.readthedocs.io", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "nonpareil", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil", - "Galaxy wrapper version": "3.1.1", - "Conda id": "nonpareil", - "Conda version": "3.4.1", - "EDAM operation (no superclasses)": [ - "Operation" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "novoplasty", - "Galaxy tool ids": [ - "novoplasty" - ], - "Description": "NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ndierckx/NOVOPlasty", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "novoplasty", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty", - "Galaxy wrapper version": "4.3.1", - "Conda id": "novoplasty", - "Conda version": "4.3.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "nugen_nudup", - "Galaxy tool ids": [ - "nugen_nudup" - ], - "Description": "Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.", - "bio.tool id": "nudup", - "bio.tool ids": [ - "nudup" - ], - "biii": null, - "bio.tool name": "NuDup", - "bio.tool description": "Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.", - "EDAM operation": [ - "Duplication detection" - ], - "EDAM topic": [ - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/tecangenomics/nudup", - "ToolShed categories": [ - "SAM", - "Metagenomics", - "Sequence Analysis", - "Transcriptomics" - ], - "ToolShed id": "nugen_nudup", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup", - "Galaxy wrapper version": "2.3.3", - "Conda id": "nudup", - "Conda version": "2.3.3", - "EDAM operation (no superclasses)": [ - "Duplication detection" - ], - "EDAM topic (no superclasses)": [ - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "obitools", - "Galaxy tool ids": [ - "obi_illumina_pairend", - "obi_ngsfilter", - "obi_annotate", - "obi_clean", - "obi_convert", - "obi_grep", - "obi_sort", - "obi_stat", - "obi_tab", - "obi_uniq" - ], - "Description": "OBITools is a set of programs developed to simplify the manipulation of sequence files", - "bio.tool id": "obitools", - "bio.tool ids": [ - "obitools" - ], - "biii": null, - "bio.tool name": "OBITools", - "bio.tool description": "Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.", - "EDAM operation": [ - "Sequence analysis", - "Sequence analysis" - ], - "EDAM topic": [ - "Sequence analysis", - "DNA", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "http://metabarcoding.org/obitools", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "obitools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools", - "Galaxy wrapper version": "1.2.13", - "Conda id": "obitools", - "Conda version": "1.2.13", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "DNA", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 10, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 10 - }, - { - "Galaxy wrapper id": "ococo", - "Galaxy tool ids": [ - "ococo" - ], - "Description": "Variant detection of SNVs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/karel-brinda/ococo", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "ococo", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo", - "Galaxy wrapper version": "0.1.2.6", - "Conda id": "ococo", - "Conda version": "0.1.2.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "odgi", - "Galaxy tool ids": [ - "odgi_build", - "odgi_viz" - ], - "Description": "Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/vgteam/odgi", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi", - "Galaxy wrapper version": "0.3", - "Conda id": "odgi", - "Conda version": "0.8.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "omark", - "Galaxy tool ids": [ - "omark" - ], - "Description": "Proteome quality assessment software", - "bio.tool id": "omark", - "bio.tool ids": [ - "omark" - ], - "biii": null, - "bio.tool name": "OMArk", - "bio.tool description": "Proteome quality assessment software", - "EDAM operation": [ - "Sequence assembly validation", - "Differential protein expression profiling" - ], - "EDAM topic": [ - "Proteomics", - "Sequence analysis", - "Statistics and probability" - ], - "Status": "To update", - "Source": "https://github.com/DessimozLab/OMArk", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "omark", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark", - "Galaxy wrapper version": "0.3.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Sequence assembly validation", - "Differential protein expression profiling" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Sequence analysis", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ont_fast5_api", - "Galaxy tool ids": [ - "ont_fast5_api_compress_fast5", - "ont_fast5_api_fast5_subset", - "ont_fast5_api_multi_to_single_fast5", - "ont_fast5_api_single_to_multi_fast5" - ], - "Description": "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nanoporetech/ont_fast5_api/", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "ont_fast5_api", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api", - "Galaxy wrapper version": "3.1.3", - "Conda id": "ont-fast5-api", - "Conda version": "4.1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "onto_toolkit", - "Galaxy tool ids": [ - "onto_tk_get_ancestor_terms", - "onto_tk_get_child_terms", - "onto_tk_get_descendent_terms", - "onto_tk_get_parent_terms", - "onto_tk_get_parent_terms_by_relationship_type", - "onto_tk_get_relationship_id_vs_relationship_def", - "onto_tk_get_relationship_id_vs_relationship_name", - "onto_tk_get_relationship_id_vs_relationship_namespace", - "onto_tk_get_relationship_types", - "onto_tk_get_root_terms", - "onto_tk_get_subontology_from", - "onto_tk_term_id_vs_term_def", - "onto_tk_term_id_vs_term_name", - "onto_tk_get_term_synonyms", - "onto_tk_get_terms", - "onto_tk_get_terms_by_relationship_type", - "onto_tk_obo2owl", - "onto_tk_obo2rdf", - "onto_tk_term_id_vs_term_def" - ], - "Description": "ONTO-Toolkit is a collection of tools for managing ontologies.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://search.cpan.org/~easr/ONTO-PERL-1.45/", - "ToolShed categories": [ - "Ontology Manipulation" - ], - "ToolShed id": "onto_toolkit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit", - "Galaxy wrapper version": "1.45", - "Conda id": "perl-onto-perl", - "Conda version": "1.45", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 17, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "optdoe", - "Galaxy tool ids": [ - "optdoe" - ], - "Description": "Optimal Design Of Experiment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/pablocarb/doebase", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "optdoe", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe", - "Galaxy wrapper version": "v2.0.2", - "Conda id": "doebase", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "optitype", - "Galaxy tool ids": [ - "optitype" - ], - "Description": "Precision HLA typing from NGS data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/FRED-2/OptiType", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "optitype", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype", - "Galaxy wrapper version": "1.3.5", - "Conda id": "optitype", - "Conda version": "1.3.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "orfipy", - "Galaxy tool ids": [ - "orfipy" - ], - "Description": "Galaxy wrapper for ORFIPY", - "bio.tool id": "orfipy", - "bio.tool ids": [ - "orfipy" - ], - "biii": null, - "bio.tool name": "orfipy", - "bio.tool description": "A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.", - "EDAM operation": [ - "Coding region prediction", - "Database search", - "Transcriptome assembly", - "De-novo assembly" - ], - "EDAM topic": [ - "Computer science", - "RNA-Seq", - "Transcriptomics", - "Small molecules" - ], - "Status": "Up-to-date", - "Source": "https://github.com/urmi-21/orfipy", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "orfipy", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy", - "Galaxy wrapper version": "0.0.4", - "Conda id": "orfipy", - "Conda version": "0.0.4", - "EDAM operation (no superclasses)": [ - "Coding region prediction", - "Database search", - "Transcriptome assembly", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Computer science", - "RNA-Seq", - "Transcriptomics", - "Small molecules" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "orthofinder", - "Galaxy tool ids": [ - "orthofinder_onlygroups" - ], - "Description": "Accurate inference of orthologous gene groups made easy", - "bio.tool id": "OrthoFinder", - "bio.tool ids": [ - "OrthoFinder" - ], - "biii": null, - "bio.tool name": "OrthoFinder", - "bio.tool description": "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.", - "EDAM operation": [ - "Genome comparison", - "Phylogenetic tree generation (from molecular sequences)", - "Phylogenetic tree analysis", - "Genome alignment" - ], - "EDAM topic": [ - "Phylogenetics", - "Phylogenomics", - "Bioinformatics", - "Comparative genomics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/davidemms/OrthoFinder", - "ToolShed categories": [ - "Phylogenetics", - "Sequence Analysis" - ], - "ToolShed id": "orthofinder", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder", - "Galaxy wrapper version": "2.5.5", - "Conda id": "orthofinder", - "Conda version": "2.5.5", - "EDAM operation (no superclasses)": [ - "Genome comparison", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics", - "Phylogenomics", - "Bioinformatics", - "Comparative genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "packaged_annotation_loader", - "Galaxy tool ids": [ - "packaged_annotation_loader" - ], - "Description": "Tool to make cached genome annotation data available as a list of datasets collection", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "packaged_annotation_loader", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader", - "Galaxy wrapper version": "0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pairtools", - "Galaxy tool ids": [ - "pairtools_dedup", - "pairtools_parse", - "pairtools_sort", - "pairtools_split", - "pairtools_stats" - ], - "Description": "Flexible tools for Hi-C data processing", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://pairtools.readthedocs.io", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pairtools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/open2c/pairtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools", - "Galaxy wrapper version": "1.1.0", - "Conda id": "pairtools", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pangolin", - "Galaxy tool ids": [ - "pangolin" - ], - "Description": "Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.", - "bio.tool id": "pangolin_cov-lineages", - "bio.tool ids": [ - "pangolin_cov-lineages" - ], - "biii": null, - "bio.tool name": "pangolin", - "bio.tool description": "Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages", - "EDAM operation": [ - "Tree-based sequence alignment", - "Variant classification" - ], - "EDAM topic": [ - "Virology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/cov-lineages/pangolin", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pangolin", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin", - "Galaxy wrapper version": "4.3", - "Conda id": "pangolin", - "Conda version": "4.3", - "EDAM operation (no superclasses)": [ - "Tree-based sequence alignment", - "Variant classification" - ], - "EDAM topic (no superclasses)": [ - "Virology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "parse_mito_blast", - "Galaxy tool ids": [ - "parse_mito_blast" - ], - "Description": "Filtering blast out from querying assembly against mitochondrial database.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "parse_mito_blast", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast", - "Galaxy wrapper version": "1.0.2", - "Conda id": "parse_mito_blast", - "Conda version": "1.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pathview", - "Galaxy tool ids": [ - "pathview" - ], - "Description": "Pathview is a tool set for pathway based data integration and visualization.", - "bio.tool id": "pathview", - "bio.tool ids": [ - "pathview" - ], - "biii": null, - "bio.tool name": "pathview", - "bio.tool description": "Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.", - "EDAM operation": [ - "Pathway or network analysis", - "Pathway or network visualisation" - ], - "EDAM topic": [ - "Molecular interactions, pathways and networks", - "Systems biology", - "Data visualisation" - ], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/pathview.html", - "ToolShed categories": [ - "Statistics", - "RNA", - "Micro-array Analysis" - ], - "ToolShed id": "pathview", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview", - "Galaxy wrapper version": "1.34.0", - "Conda id": "bioconductor-pathview", - "Conda version": "1.42.0", - "EDAM operation (no superclasses)": [ - "Pathway or network analysis", - "Pathway or network visualisation" - ], - "EDAM topic (no superclasses)": [ - "Molecular interactions, pathways and networks", - "Systems biology", - "Data visualisation" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pbgcpp", - "Galaxy tool ids": [ - "pbgcpp" - ], - "Description": "Compute genomic consensus and call variants using PacBio reads mapped to a reference", - "bio.tool id": "genomicconsensus", - "bio.tool ids": [ - "genomicconsensus" - ], - "biii": null, - "bio.tool name": "GenomicConsensus", - "bio.tool description": "The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.", - "EDAM operation": [ - "Variant calling" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/PacificBiosciences/gcpp", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pbgcpp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp", - "Galaxy wrapper version": "2.0.2", - "Conda id": "pbgcpp", - "Conda version": "2.0.2", - "EDAM operation (no superclasses)": [ - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pbmm2", - "Galaxy tool ids": [ - "pbmm2" - ], - "Description": "A minimap2 SMRT wrapper for PacBio data.", - "bio.tool id": "pbmm2", - "bio.tool ids": [ - "pbmm2" - ], - "biii": null, - "bio.tool name": "pbmm2", - "bio.tool description": "pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.", - "EDAM operation": [ - "Pairwise sequence alignment", - "Sorting" - ], - "EDAM topic": [ - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/PacificBiosciences/pbmm2", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "pbmm2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2", - "Galaxy wrapper version": "1.13.1", - "Conda id": "pbmm2", - "Conda version": "1.13.1", - "EDAM operation (no superclasses)": [ - "Pairwise sequence alignment", - "Sorting" - ], - "EDAM topic (no superclasses)": [ - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pbtk", - "Galaxy tool ids": [ - "bam2fastx" - ], - "Description": "Convert PacBio Bam File to fasta or fastq file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/PacificBiosciences/pbtk", - "ToolShed categories": [ - "Convert Formats", - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "bam2fastx", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk", - "Galaxy wrapper version": "3.1.1", - "Conda id": "pbtk", - "Conda version": "3.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pe_histogram", - "Galaxy tool ids": [ - "pe_histogram" - ], - "Description": "Contains a tool that produces an insert size histogram for a paired-end BAM file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram", - "ToolShed categories": [ - "Graphics" - ], - "ToolShed id": "pe_histogram", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram", - "Galaxy wrapper version": "1.0.1", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "peakzilla", - "Galaxy tool ids": [ - "peakzilla" - ], - "Description": "Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/steinmann/peakzilla", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "peakzilla", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla", - "Galaxy wrapper version": "1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pear", - "Galaxy tool ids": [ - "iuc_pear" - ], - "Description": "PEAR evaluates all possible paired-end read overlaps", - "bio.tool id": "pear", - "bio.tool ids": [ - "pear" - ], - "biii": null, - "bio.tool name": "PEAR", - "bio.tool description": "Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.", - "EDAM operation": [ - "Sequence merging" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "pear", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear", - "Galaxy wrapper version": "0.9.6", - "Conda id": "pear", - "Conda version": "0.9.6", - "EDAM operation (no superclasses)": [ - "Sequence merging" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pharokka", - "Galaxy tool ids": [ - "pharokka" - ], - "Description": "rapid standardised annotation tool for bacteriophage genomes and metagenomes", - "bio.tool id": "pharokka", - "bio.tool ids": [ - "pharokka" - ], - "biii": null, - "bio.tool name": "Pharokka", - "bio.tool description": "Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.", - "EDAM operation": [ - "Genome annotation", - "Antimicrobial resistance prediction", - "tRNA gene prediction", - "Formatting", - "Sequence assembly" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence sites, features and motifs", - "Workflows", - "Functional, regulatory and non-coding RNA" - ], - "Status": "To update", - "Source": "https://github.com/gbouras13/pharokka", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "pharokka", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", - "Galaxy wrapper version": "1.3.2", - "Conda id": "\n pharokka\n ", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Genome annotation", - "Antimicrobial resistance prediction", - "tRNA gene prediction", - "Formatting", - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence sites, features and motifs", - "Workflows", - "Functional, regulatory and non-coding RNA" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "phyloseq", - "Galaxy tool ids": [ - "phyloseq_from_biom", - "phyloseq_from_dada2", - "phyloseq_plot_ordination", - "phyloseq_plot_richness" - ], - "Description": "Handling and analysis of high-throughput microbiome census data", - "bio.tool id": "phyloseq", - "bio.tool ids": [ - "phyloseq" - ], - "biii": null, - "bio.tool name": "phyloseq", - "bio.tool description": "Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.", - "EDAM operation": [ - "Deposition", - "Analysis", - "Visualisation" - ], - "EDAM topic": [ - "Microbiology", - "Sequence analysis", - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "phyloseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq", - "Galaxy wrapper version": "1.46.0", - "Conda id": "bioconductor-phyloseq", - "Conda version": "1.46.0", - "EDAM operation (no superclasses)": [ - "Deposition", - "Analysis", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Sequence analysis", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "phyml", - "Galaxy tool ids": [ - "phyml" - ], - "Description": "PhyML is a phylogeny software based on the maximum-likelihood principle.", - "bio.tool id": "phyml", - "bio.tool ids": [ - "phyml" - ], - "biii": null, - "bio.tool name": "PhyML", - "bio.tool description": "Phylogenetic estimation software using Maximum Likelihood", - "EDAM operation": [ - "Phylogenetic tree generation (maximum likelihood and Bayesian methods)" - ], - "EDAM topic": [ - "Phylogenetics", - "Bioinformatics", - "Phylogenetics" - ], - "Status": "Up-to-date", - "Source": "http://www.atgc-montpellier.fr/phyml/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "phyml", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml", - "Galaxy wrapper version": "3.3.20220408", - "Conda id": "phyml", - "Conda version": "3.3.20220408", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Phylogenetics", - "Bioinformatics", - "Phylogenetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "picard", - "Galaxy tool ids": [ - "picard_AddCommentsToBam", - "picard_AddOrReplaceReadGroups", - "picard_BedToIntervalList", - "picard_CleanSam", - "picard_CASM", - "picard_CollectBaseDistributionByCycle", - "picard_CollectGcBiasMetrics", - "picard_CollectHsMetrics", - "picard_CollectInsertSizeMetrics", - "picard_CollectRnaSeqMetrics", - "picard_artifact_metrics", - "picard_CollectWgsMetrics", - "picard_DownsampleSam", - "picard_EstimateLibraryComplexity", - "picard_FastqToSam", - "picard_FilterSamReads", - "picard_FixMateInformation", - "picard_MarkDuplicates", - "picard_MarkDuplicatesWithMateCigar", - "picard_MeanQualityByCycle", - "picard_MergeBamAlignment", - "picard_MergeSamFiles", - "picard_NormalizeFasta", - "picard_QualityScoreDistribution", - "picard_ReorderSam", - "picard_ReplaceSamHeader", - "picard_RevertOriginalBaseQualitiesAndAddMateCigar", - "picard_RevertSam", - "picard_SamToFastq", - "picard_SortSam", - "picard_ValidateSamFile" - ], - "Description": "Picard SAM/BAM manipulation tools.", - "bio.tool id": "picard_samtofastq", - "bio.tool ids": [ - "picard_samtofastq", - "picard_fastqtosam", - "picard_reordersam", - "picard_replacesamheader" - ], - "biii": null, - "bio.tool name": "picard_samtofastq", - "bio.tool description": "Create a FASTQ file.", - "EDAM operation": [ - "Formatting" - ], - "EDAM topic": [ - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "http://broadinstitute.github.io/picard/", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "picard", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard", - "Galaxy wrapper version": "3.1.1", - "Conda id": "picard", - "Conda version": "3.1.1", - "EDAM operation (no superclasses)": [ - "Formatting" - ], - "EDAM topic (no superclasses)": [ - "Sequencing" - ], - "Available on UseGalaxy.org": 31, - "Available on UseGalaxy.org.au": 31, - "Available on UseGalaxy.eu": 31, - "Available on UseGalaxy.org.fr": 31 - }, - { - "Galaxy wrapper id": "pick_value", - "Galaxy tool ids": [ - "pick_value" - ], - "Description": "Compose a text parameter value using text, integer and float values", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "pick_value", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value", - "Galaxy wrapper version": "0.2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "picrust", - "Galaxy tool ids": [ - "picrust_categorize", - "picrust_compare_biom", - "picrust_format_tree_and_trait_table", - "picrust_metagenome_contributions", - "picrust_normalize_by_copy_number", - "picrust_predict_metagenomes" - ], - "Description": "PICRUSt wrappers", - "bio.tool id": "picrust", - "bio.tool ids": [ - "picrust" - ], - "biii": null, - "bio.tool name": "PICRUSt", - "bio.tool description": "PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.", - "EDAM operation": [ - "Phylogenetic reconstruction", - "Expression analysis", - "Genome annotation", - "DNA barcoding" - ], - "EDAM topic": [ - "Metagenomics", - "Microbial ecology", - "Functional, regulatory and non-coding RNA", - "Metagenomic sequencing" - ], - "Status": "To update", - "Source": "https://picrust.github.io/picrust/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "picrust", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust", - "Galaxy wrapper version": "1.1.1", - "Conda id": "picrust", - "Conda version": "1.1.4", - "EDAM operation (no superclasses)": [ - "Phylogenetic reconstruction", - "Expression analysis", - "Genome annotation", - "DNA barcoding" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbial ecology", - "Functional, regulatory and non-coding RNA", - "Metagenomic sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "picrust2", - "Galaxy tool ids": [ - "picrust2_add_descriptions", - "picrust2_hsp", - "picrust2_metagenome_pipeline", - "picrust2_pathway_pipeline", - "picrust2_pipeline", - "picrust2_place_seqs", - "picrust2_shuffle_predictions" - ], - "Description": "PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States", - "bio.tool id": "picrust2", - "bio.tool ids": [ - "picrust2" - ], - "biii": null, - "bio.tool name": "PICRUSt2", - "bio.tool description": "PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.", - "EDAM operation": [ - "Phylogenetic reconstruction", - "Expression analysis", - "Rarefaction", - "Pathway analysis" - ], - "EDAM topic": [ - "Metagenomics", - "Microbiology", - "Phylogenetics", - "Metagenomic sequencing" - ], - "Status": "To update", - "Source": "https://github.com/picrust/picrust2/wiki", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "picrust2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/picrust/picrust2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2", - "Galaxy wrapper version": "2.5.1", - "Conda id": "picrust2", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "Phylogenetic reconstruction", - "Expression analysis", - "Rarefaction", - "Pathway analysis" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbiology", - "Phylogenetics", - "Metagenomic sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 7, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pilon", - "Galaxy tool ids": [ - "pilon" - ], - "Description": "pilon is a tool for assembly improvement and variant analysis in bacteria", - "bio.tool id": "pilon", - "bio.tool ids": [ - "pilon" - ], - "biii": null, - "bio.tool name": "pilon", - "bio.tool description": "Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.", - "EDAM operation": [ - "Sequence assembly", - "Analysis", - "Read alignment" - ], - "EDAM topic": [ - "Assembly" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pilon", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon", - "Galaxy wrapper version": "1.20.1", - "Conda id": "pilon", - "Conda version": "1.24", - "EDAM operation (no superclasses)": [ - "Sequence assembly", - "Analysis" - ], - "EDAM topic (no superclasses)": [ - "Assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pipelign", - "Galaxy tool ids": [ - "pipelign" - ], - "Description": "Multipe sequence alignment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/asmmhossain/pipelign/", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "pipelign", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign", - "Galaxy wrapper version": "0.2", - "Conda id": "pipelign", - "Conda version": "0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pizzly", - "Galaxy tool ids": [ - "pizzly" - ], - "Description": "Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/pmelsted/pizzly/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly", - "Galaxy wrapper version": "0.37.3.1", - "Conda id": "pizzly", - "Conda version": "0.37.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plasflow", - "Galaxy tool ids": [ - "PlasFlow" - ], - "Description": "PlasFlow - Prediction of plasmid sequences in metagenomic contigs.", - "bio.tool id": "plasflow", - "bio.tool ids": [ - "plasflow" - ], - "biii": null, - "bio.tool name": "PlasFlow", - "bio.tool description": "PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.", - "EDAM operation": [ - "Sequence analysis" - ], - "EDAM topic": [ - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/smaegol/PlasFlow", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "plasflow", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow", - "Galaxy wrapper version": "1.1.0", - "Conda id": "plasflow", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [ - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "plasmidfinder", - "Galaxy tool ids": [ - "plasmidfinder" - ], - "Description": "\"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage\"", - "bio.tool id": "PlasmidFinder", - "bio.tool ids": [ - "PlasmidFinder" - ], - "biii": null, - "bio.tool name": "PlasmidFinder", - "bio.tool description": "PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).", - "EDAM operation": [ - "Genome assembly", - "Scaffolding", - "Multilocus sequence typing" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Sequence assembly", - "Mapping", - "Probes and primers" - ], - "Status": "Up-to-date", - "Source": "https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "plasmidfinder", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder", - "Galaxy wrapper version": "2.1.6", - "Conda id": "plasmidfinder", - "Conda version": "2.1.6", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Scaffolding", - "Multilocus sequence typing" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Sequence assembly", - "Mapping", - "Probes and primers" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "plink", - "Galaxy tool ids": [ - "plink" - ], - "Description": "PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "bio.tool id": "plink", - "bio.tool ids": [ - "plink" - ], - "biii": null, - "bio.tool name": "PLINK", - "bio.tool description": "Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", - "EDAM operation": [ - "Genetic variation analysis" - ], - "EDAM topic": [ - "GWAS study" - ], - "Status": "Up-to-date", - "Source": "https://www.cog-genomics.org/plink", - "ToolShed categories": [ - "Genome-Wide Association Study" - ], - "ToolShed id": "plink", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink", - "Galaxy wrapper version": "1.90b6.21", - "Conda id": "plink", - "Conda version": "1.90b6.21", - "EDAM operation (no superclasses)": [ - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "GWAS study" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "polypolish", - "Galaxy tool ids": [ - "polypolish" - ], - "Description": "\"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.\"", - "bio.tool id": "Polypolish", - "bio.tool ids": [ - "Polypolish" - ], - "biii": null, - "bio.tool name": "Polypolish", - "bio.tool description": "Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.", - "EDAM operation": [ - "Genome assembly", - "Read mapping", - "Mapping assembly", - "Sequencing error detection" - ], - "EDAM topic": [ - "Sequence assembly", - "Sequence composition, complexity and repeats", - "Mapping" - ], - "Status": "To update", - "Source": "https://github.com/rrwick/Polypolish", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "polypolish", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish", - "Galaxy wrapper version": "0.5.0", - "Conda id": "polypolish", - "Conda version": "0.6.0", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Read mapping", - "Mapping assembly", - "Sequencing error detection" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Sequence composition, complexity and repeats", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "porechop", - "Galaxy tool ids": [ - "porechop" - ], - "Description": "Porechop - Finding and removing adapters from Oxford Nanopore reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/rrwick/Porechop", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "porechop", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop", - "Galaxy wrapper version": null, - "Conda id": "porechop", - "Conda version": "0.2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "poretools", - "Galaxy tool ids": [ - "poretools_events", - "poretools_extract", - "poretools_hist", - "poretools_nucdist", - "poretools_occupancy", - "poretools_qualdist", - "poretools_qualpos", - "poretools_squiggle", - "poretools_stats", - "poretools_tabular", - "poretools_times", - "poretools_winner", - "poretools_yield_plot" - ], - "Description": "A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.", - "bio.tool id": "poretools", - "bio.tool ids": [ - "poretools" - ], - "biii": null, - "bio.tool name": "Poretools", - "bio.tool description": "Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.", - "EDAM operation": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic": [ - "DNA", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://poretools.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools", - "Galaxy wrapper version": "0.6.1a1", - "Conda id": "poretools", - "Conda version": "0.6.1a1", - "EDAM operation (no superclasses)": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "DNA", - "Sequencing" - ], - "Available on UseGalaxy.org": 13, - "Available on UseGalaxy.org.au": 13, - "Available on UseGalaxy.eu": 13, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "presto", - "Galaxy tool ids": [ - "presto_alignsets", - "presto_assemblepairs", - "presto_buildconsensus", - "presto_collapseseq", - "presto_filterseq", - "presto_maskprimers", - "presto_pairseq", - "presto_parseheaders", - "presto_parselog", - "presto_partition", - "prestor_abseq3" - ], - "Description": "pRESTO toolkit for immune repertoire analysis.", - "bio.tool id": "presto", - "bio.tool ids": [ - "presto" - ], - "biii": null, - "bio.tool name": "pRESTO", - "bio.tool description": "Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.", - "EDAM operation": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic": [ - "Sequencing", - "DNA", - "Immunology" - ], - "Status": "To update", - "Source": "https://presto.readthedocs.io/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "presto", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto", - "Galaxy wrapper version": "0.6.2", - "Conda id": "presto", - "Conda version": "0.7.2", - "EDAM operation (no superclasses)": [ - "Nucleic acid sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "DNA", - "Immunology" - ], - "Available on UseGalaxy.org": 11, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pretext", - "Galaxy tool ids": [ - "pretext_graph", - "pretext_map", - "pretext_snapshot" - ], - "Description": "Process genome contacts maps processing images.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/wtsi-hpag/PretextSnapshot", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "suite_pretext", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext", - "Galaxy wrapper version": "0.0.6", - "Conda id": "pretextgraph", - "Conda version": "0.0.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "prinseq", - "Galaxy tool ids": [ - "prinseq" - ], - "Description": "PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets", - "bio.tool id": "prinseq", - "bio.tool ids": [ - "prinseq" - ], - "biii": null, - "bio.tool name": "PRINSEQ", - "bio.tool description": "PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.", - "EDAM operation": [ - "Read pre-processing", - "Sequence trimming", - "Sequence contamination filtering" - ], - "EDAM topic": [ - "Transcriptomics", - "Metagenomics", - "Genomics" - ], - "Status": "To update", - "Source": "http://prinseq.sourceforge.net/manual.html", - "ToolShed categories": [ - "Fastq Manipulation", - "Metagenomics" - ], - "ToolShed id": "prinseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq", - "Galaxy wrapper version": "@TOOL_VERSION+galaxy2", - "Conda id": "prinseq", - "Conda version": "0.20.4", - "EDAM operation (no superclasses)": [ - "Read pre-processing", - "Sequence trimming", - "Sequence contamination filtering" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "prodigal", - "Galaxy tool ids": [ - "prodigal" - ], - "Description": "A protein-coding gene prediction software tool for bacterial and archaeal genomes", - "bio.tool id": "prodigal", - "bio.tool ids": [ - "prodigal" - ], - "biii": null, - "bio.tool name": "Prodigal", - "bio.tool description": "Fast, reliable protein-coding gene prediction for prokaryotic genomes.", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Genomics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/hyattpd/Prodigal", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "prodigal", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal", - "Galaxy wrapper version": "2.6.3", - "Conda id": "prodigal", - "Conda version": "2.6.3", - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "progressivemauve", - "Galaxy tool ids": [ - "progressivemauve", - "xmfa2gff3" - ], - "Description": "Mauve/ProgressiveMauve Multiple Sequence Aligner", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "progressivemauve", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve", - "Galaxy wrapper version": null, - "Conda id": "progressivemauve", - "Conda version": "snapshot_2015_02_13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "prokka", - "Galaxy tool ids": [ - "prokka" - ], - "Description": "Rapid annotation of prokaryotic genomes", - "bio.tool id": "prokka", - "bio.tool ids": [ - "prokka" - ], - "biii": null, - "bio.tool name": "Prokka", - "bio.tool description": "Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.", - "EDAM operation": [ - "Gene prediction", - "Coding region prediction", - "Genome annotation" - ], - "EDAM topic": [ - "Genomics", - "Model organisms", - "Virology" - ], - "Status": "Up-to-date", - "Source": "http://github.com/tseemann/prokka", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "prokka", - "Galaxy wrapper owner": "crs4", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka", - "Galaxy wrapper version": "1.14.6", - "Conda id": "prokka", - "Conda version": "1.14.6", - "EDAM operation (no superclasses)": [ - "Coding region prediction", - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Model organisms", - "Virology" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "prot-scriber", - "Galaxy tool ids": [ - "prot_scriber" - ], - "Description": "Protein annotation of short human readable descriptions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/usadellab/prot-scriber", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "prot_scriber", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber", - "Galaxy wrapper version": "0.1.5", - "Conda id": "prot-scriber", - "Conda version": "0.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteinortho", - "Galaxy tool ids": [ - "proteinortho", - "proteinortho_grab_proteins", - "proteinortho_summary" - ], - "Description": "Proteinortho is a tool to detect orthologous proteins/genes within different species.", - "bio.tool id": "proteinortho", - "bio.tool ids": [ - "proteinortho" - ], - "biii": null, - "bio.tool name": "Proteinortho", - "bio.tool description": "Proteinortho is a tool to detect orthologous genes within different species", - "EDAM operation": [ - "Sequence clustering", - "Sequence analysis" - ], - "EDAM topic": [ - "Comparative genomics" - ], - "Status": "Up-to-date", - "Source": "https://gitlab.com/paulklemm_PHD/proteinortho", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteinortho", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://gitlab.com/paulklemm_PHD/proteinortho", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho", - "Galaxy wrapper version": "6.3.1", - "Conda id": "proteinortho", - "Conda version": "6.3.1", - "EDAM operation (no superclasses)": [ - "Sequence clustering", - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Comparative genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "psiclass", - "Galaxy tool ids": [ - "psiclass" - ], - "Description": "PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.", - "bio.tool id": "psiclass", - "bio.tool ids": [ - "psiclass" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/splicebox/PsiCLASS", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "psiclass", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass", - "Galaxy wrapper version": "1.0.3", - "Conda id": "psiclass", - "Conda version": "1.0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pureclip", - "Galaxy tool ids": [ - "pureclip" - ], - "Description": "PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/skrakau/PureCLIP", - "ToolShed categories": [ - "Sequence Analysis", - "RNA", - "CLIP-seq" - ], - "ToolShed id": "pureclip", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip", - "Galaxy wrapper version": "1.0.4", - "Conda id": "pureclip", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "purge_dups", - "Galaxy tool ids": [ - "purge_dups" - ], - "Description": "Purge haplotigs and overlaps in an assembly based on read depth", - "bio.tool id": "purge_dups", - "bio.tool ids": [ - "purge_dups" - ], - "biii": null, - "bio.tool name": "purge_dups", - "bio.tool description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", - "EDAM operation": [ - "Genome assembly", - "Read binning", - "Scaffolding" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/dfguan/purge_dups", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "purge_dups", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups", - "Galaxy wrapper version": "1.2.6", - "Conda id": "purge_dups", - "Conda version": "1.2.6", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Read binning", - "Scaffolding" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pycoqc", - "Galaxy tool ids": [ - "pycoqc" - ], - "Description": "QC metrics for ONT Basecalling", - "bio.tool id": "pycoqc", - "bio.tool ids": [ - "pycoqc" - ], - "biii": null, - "bio.tool name": "pycoQC", - "bio.tool description": "PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.", - "EDAM operation": [ - "Sequencing quality control", - "Statistical calculation" - ], - "EDAM topic": [ - "Sequence analysis", - "Data quality management", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/tleonardi/pycoQC", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "pycoqc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc", - "Galaxy wrapper version": "2.5.2", - "Conda id": "pycoqc", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "Sequencing quality control", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis", - "Data quality management", - "Sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pyega3", - "Galaxy tool ids": [ - "pyega3" - ], - "Description": "EGA python client uses the EGA REST API to download authorized datasets and files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/EGA-archive/ega-download-client", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "ega_download_client", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3", - "Galaxy wrapper version": "5.0.2", - "Conda id": "pyega3", - "Conda version": "5.2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pygenometracks", - "Galaxy tool ids": [ - "pygenomeTracks" - ], - "Description": "pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.", - "bio.tool id": "pygenometracks", - "bio.tool ids": [ - "pygenometracks" - ], - "biii": null, - "bio.tool name": "pyGenomeTracks", - "bio.tool description": "reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.", - "EDAM operation": [ - "Visualisation", - "Formatting" - ], - "EDAM topic": [ - "Model organisms", - "Imaging", - "Workflows" - ], - "Status": "To update", - "Source": "https://github.com/deeptools/pyGenomeTracks", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "pygenometracks", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks", - "Galaxy wrapper version": "3.8", - "Conda id": "pygenometracks", - "Conda version": "3.9", - "EDAM operation (no superclasses)": [ - "Visualisation", - "Formatting" - ], - "EDAM topic (no superclasses)": [ - "Model organisms", - "Imaging", - "Workflows" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "pysradb", - "Galaxy tool ids": [ - "pysradb_search" - ], - "Description": "pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.", - "bio.tool id": "pysradb", - "bio.tool ids": [ - "pysradb" - ], - "biii": null, - "bio.tool name": "pysradb", - "bio.tool description": "Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.", - "EDAM operation": [ - "Deposition", - "Data retrieval" - ], - "EDAM topic": [ - "Sequencing", - "Gene transcripts", - "Bioinformatics" - ], - "Status": "To update", - "Source": "https://github.com/saketkc/pysradb", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "pysradb_search", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb", - "Galaxy wrapper version": "1.4.2", - "Conda id": "pysradb", - "Conda version": "2.2.0", - "EDAM operation (no superclasses)": [ - "Deposition", - "Data retrieval" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Gene transcripts", - "Bioinformatics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qfilt", - "Galaxy tool ids": [ - "qfilt" - ], - "Description": "Filter sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/veg/qfilt", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "qfilt", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt", - "Galaxy wrapper version": "1.0.0+galaxy1", - "Conda id": "qfilt", - "Conda version": "0.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qiime_add_on", - "Galaxy tool ids": [ - "qiime_collapse_samples", - "qiime_make_otu_table" - ], - "Description": "QIIME to perform microbial community analysis", - "bio.tool id": "qiime_add_on", - "bio.tool ids": [ - "qiime_add_on", - "qiime_core" - ], - "biii": null, - "bio.tool name": "qiime_add_on", - "bio.tool description": "QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.", - "EDAM operation": [ - "Demultiplexing", - "Visualisation", - "Taxonomic classification", - "Phylogenetic analysis", - "Sequencing quality control" - ], - "EDAM topic": [ - "Microbial ecology", - "Phylogeny", - "Metagenomics", - "Metatranscriptomics" - ], - "Status": "To update", - "Source": "http://www.qiime.org", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "qiime", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on", - "Galaxy wrapper version": null, - "Conda id": "qiime", - "Conda version": "1.9.1", - "EDAM operation (no superclasses)": [ - "Demultiplexing", - "Visualisation", - "Taxonomic classification", - "Phylogenetic analysis", - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Microbial ecology", - "Phylogeny", - "Metagenomics", - "Metatranscriptomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "qiime_core", - "Galaxy tool ids": [ - "qiime_align_seqs", - "qiime_alpha_diversity", - "qiime_alpha_rarefaction", - "qiime_assign_taxonomy", - "qiime_beta_diversity", - "qiime_beta_diversity_through_plots", - "qiime_compare_categories", - "qiime_core_diversity", - "qiime_count_seqs", - "qiime_extract_barcodes", - "qiime_filter_alignment", - "qiime_filter_fasta", - "qiime_filter_otus_from_otu_table", - "qiime_filter_samples_from_otu_table", - "qiime_filter_taxa_from_otu_table", - "qiime_jackknifed_beta_diversity", - "qiime_make_emperor", - "qiime_make_otu_heatmap", - "qiime_make_phylogeny", - "qiime_multiple_join_paired_ends", - "qiime_multiple_split_libraries_fastq", - "qiime_pick_closed_reference_otus", - "qiime_pick_open_reference_otus", - "qiime_pick_otus", - "qiime_pick_rep_set", - "qiime_plot_taxa_summary", - "qiime_split_libraries", - "qiime_split_libraries_fastq", - "qiime_summarize_taxa", - "qiime_summarize_taxa_through_plots", - "qiime_upgma_cluster", - "qiime_validate_mapping_file" - ], - "Description": "QIIME to perform microbial community analysis", - "bio.tool id": "qiime_core", - "bio.tool ids": [ - "qiime_core" - ], - "biii": null, - "bio.tool name": "qiime_core", - "bio.tool description": "QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.", - "EDAM operation": [ - "Demultiplexing", - "Visualisation", - "Taxonomic classification", - "Phylogenetic analysis", - "Sequencing quality control" - ], - "EDAM topic": [ - "Microbial ecology", - "Phylogeny", - "Metagenomics", - "Metatranscriptomics" - ], - "Status": "To update", - "Source": "http://www.qiime.org", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "qiime", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core", - "Galaxy wrapper version": null, - "Conda id": "qiime", - "Conda version": "1.9.1", - "EDAM operation (no superclasses)": [ - "Demultiplexing", - "Visualisation", - "Taxonomic classification", - "Phylogenetic analysis", - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Microbial ecology", - "Phylogeny", - "Metagenomics", - "Metatranscriptomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 32, - "Available on UseGalaxy.org.fr": 32 - }, - { - "Galaxy wrapper id": "qiime_extract_viz", - "Galaxy tool ids": [ - "qiime_extract_viz" - ], - "Description": "Extract vizualization from QIIME artifacts", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.qiime.org", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "qiime_extract_viz", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz", - "Galaxy wrapper version": "0.1.0", - "Conda id": "unzip", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qq_tools", - "Galaxy tool ids": [ - "qq_manhattan" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://CRAN.R-project.org/package=qqman", - "ToolShed categories": [ - "Visualization", - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools", - "Galaxy wrapper version": "0.1.0", - "Conda id": "r-qqman", - "Conda version": "0.1.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qualimap", - "Galaxy tool ids": [ - "qualimap_bamqc", - "qualimap_counts", - "qualimap_multi_bamqc", - "qualimap_rnaseq" - ], - "Description": null, - "bio.tool id": "qualimap", - "bio.tool ids": [ - "qualimap" - ], - "biii": null, - "bio.tool name": "QualiMap", - "bio.tool description": "Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.", - "EDAM operation": [ - "Sequencing quality control" - ], - "EDAM topic": [ - "Data quality management" - ], - "Status": "To update", - "Source": "http://qualimap.bioinfo.cipf.es/", - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics", - "SAM" - ], - "ToolShed id": "qualimap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap", - "Galaxy wrapper version": "2.2.2d", - "Conda id": "qualimap", - "Conda version": "2.3", - "EDAM operation (no superclasses)": [ - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Data quality management" - ], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "quast", - "Galaxy tool ids": [ - "quast" - ], - "Description": "Quast (Quality ASsessment Tool) evaluates genome assemblies.", - "bio.tool id": "quast", - "bio.tool ids": [ - "quast" - ], - "biii": null, - "bio.tool name": "QUAST", - "bio.tool description": "QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.", - "EDAM operation": [ - "Visualisation", - "Sequence assembly validation" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "http://quast.bioinf.spbau.ru/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "quast", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast", - "Galaxy wrapper version": "5.2.0", - "Conda id": "quast", - "Conda version": "5.2.0", - "EDAM operation (no superclasses)": [ - "Visualisation", - "Sequence assembly validation" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "query_impc", - "Galaxy tool ids": [ - "query_impc" - ], - "Description": "Contains a tool to query the IMPC database.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc", - "ToolShed categories": [ - "Convert Formats", - "Web Services" - ], - "ToolShed id": "query_impc", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc", - "Galaxy wrapper version": "0.9.0", - "Conda id": "requests", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "query_tabular", - "Galaxy tool ids": [ - "filter_tabular", - "query_tabular", - "sqlite_to_tabular" - ], - "Description": "Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular", - "Galaxy wrapper version": "3.3.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "quickmerge", - "Galaxy tool ids": [ - "quickmerge" - ], - "Description": "Merge long-read and hybrid assemblies to increase contiguity", - "bio.tool id": "quickmerge", - "bio.tool ids": [ - "quickmerge" - ], - "biii": null, - "bio.tool name": "quickmerge", - "bio.tool description": "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.", - "EDAM operation": [ - "Genome assembly", - "Scaffolding", - "De-novo assembly", - "Genotyping" - ], - "EDAM topic": [ - "Structural variation", - "Sequence assembly", - "DNA polymorphism", - "Whole genome sequencing", - "Genotype and phenotype" - ], - "Status": "Up-to-date", - "Source": "https://github.com/mahulchak/quickmerge", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "quickmerge", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge", - "Galaxy wrapper version": "0.3", - "Conda id": "quickmerge", - "Conda version": "0.3", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Scaffolding", - "De-novo assembly", - "Genotyping" - ], - "EDAM topic (no superclasses)": [ - "Structural variation", - "Sequence assembly", - "DNA polymorphism", - "Whole genome sequencing", - "Genotype and phenotype" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "raceid", - "Galaxy tool ids": [ - "raceid_clustering", - "raceid_filtnormconf", - "raceid_inspectclusters", - "raceid_inspecttrajectory", - "raceid_trajectory" - ], - "Description": "RaceID3, StemID2, FateID - scRNA analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/dgrun/RaceID3_StemID2_package/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid", - "Galaxy wrapper version": "0.2.3", - "Conda id": "r-raceid", - "Conda version": "0.1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ragtag", - "Galaxy tool ids": [ - "ragtag" - ], - "Description": "Reference-guided scaffolding of draft genomes tool.", - "bio.tool id": "ragtag", - "bio.tool ids": [ - "ragtag" - ], - "biii": null, - "bio.tool name": "ragtag", - "bio.tool description": "RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/malonge/RagTag", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "ragtag", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag", - "Galaxy wrapper version": "2.1.0", - "Conda id": "ragtag", - "Conda version": "2.1.0", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rapidnj", - "Galaxy tool ids": [ - "rapidnj" - ], - "Description": "Galaxy wrapper for the RapidNJ tool", - "bio.tool id": "rapidnj", - "bio.tool ids": [ - "rapidnj" - ], - "biii": null, - "bio.tool name": "RapidNJ", - "bio.tool description": "A tool for fast canonical neighbor-joining tree construction.", - "EDAM operation": [ - "Phylogenetic tree generation" - ], - "EDAM topic": [ - "Phylogeny" - ], - "Status": "Up-to-date", - "Source": "https://birc.au.dk/software/rapidnj/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "rapidnj", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj", - "Galaxy wrapper version": "2.3.2", - "Conda id": "rapidnj", - "Conda version": "2.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Phylogeny" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rasusa", - "Galaxy tool ids": [ - "rasusa" - ], - "Description": "Randomly subsample sequencing reads to a specified coverage", - "bio.tool id": "rasusa", - "bio.tool ids": [ - "rasusa" - ], - "biii": null, - "bio.tool name": "rasusa", - "bio.tool description": "Produces an unbiased subsample of your reads", - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/mbhall88/rasusa", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "rasusa", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa", - "Galaxy wrapper version": "0.8.0", - "Conda id": "rasusa", - "Conda version": "2.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "raven", - "Galaxy tool ids": [ - "raven" - ], - "Description": "Raven is a de novo genome assembler for long uncorrected reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/lbcb-sci/raven", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven", - "Galaxy wrapper version": "1.8.3", - "Conda id": "raven-assembler", - "Conda version": "1.8.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "raxml", - "Galaxy tool ids": [ - "raxml" - ], - "Description": "RAxML - A Maximum Likelihood based phylogenetic inference", - "bio.tool id": "raxml", - "bio.tool ids": [ - "raxml" - ], - "biii": null, - "bio.tool name": "RAxML", - "bio.tool description": "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.", - "EDAM operation": [ - "Sequence analysis", - "Phylogenetic tree analysis" - ], - "EDAM topic": [ - "Phylogenetics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://www.exelixis-lab.org/web/software/raxml/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "raxml", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml", - "Galaxy wrapper version": "8.2.12", - "Conda id": "raxml", - "Conda version": "8.2.13", - "EDAM operation (no superclasses)": [ - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Phylogenetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rcorrector", - "Galaxy tool ids": [ - "rcorrector" - ], - "Description": "Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.", - "bio.tool id": "rcorrector", - "bio.tool ids": [ - "rcorrector" - ], - "biii": null, - "bio.tool name": "Rcorrector", - "bio.tool description": "This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.", - "EDAM operation": [ - "Sequencing error detection" - ], - "EDAM topic": [ - "RNA", - "RNA-Seq", - "Sequencing" - ], - "Status": "To update", - "Source": "https://github.com/mourisl/Rcorrector", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "rcorrector", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector", - "Galaxy wrapper version": "1.0.3+galaxy1", - "Conda id": "rcorrector", - "Conda version": "1.0.7", - "EDAM operation (no superclasses)": [ - "Sequencing error detection" - ], - "EDAM topic (no superclasses)": [ - "RNA", - "RNA-Seq" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "read_it_and_keep", - "Galaxy tool ids": [ - "read_it_and_keep" - ], - "Description": "Rapid decontamination of SARS-CoV-2 sequencing reads", - "bio.tool id": "read_it_and_keep", - "bio.tool ids": [ - "read_it_and_keep" - ], - "biii": null, - "bio.tool name": "read_it_and_keep", - "bio.tool description": "Read contamination removal", - "EDAM operation": [ - "Filtering", - "Genome alignment" - ], - "EDAM topic": [ - "Pathology", - "Genomics" - ], - "Status": "To update", - "Source": "https://github.com/GenomePathogenAnalysisService/read-it-and-keep", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "read_it_and_keep", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep", - "Galaxy wrapper version": "0.2.2", - "Conda id": "read-it-and-keep", - "Conda version": "0.3.0", - "EDAM operation (no superclasses)": [ - "Filtering", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Pathology", - "Genomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "recentrifuge", - "Galaxy tool ids": [ - "recentrifuge" - ], - "Description": "\"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.\"", - "bio.tool id": "Recentrifuge", - "bio.tool ids": [ - "Recentrifuge" - ], - "biii": null, - "bio.tool name": "Recentrifuge", - "bio.tool description": "Robust comparative analysis and contamination removal for metagenomics.", - "EDAM operation": [ - "Taxonomic classification", - "Expression analysis", - "Cross-assembly" - ], - "EDAM topic": [ - "Metagenomics", - "Microbial ecology", - "Metagenomic sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/khyox/recentrifuge", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "recentrifuge", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge", - "Galaxy wrapper version": "1.14.0", - "Conda id": "recentrifuge", - "Conda version": "1.14.0", - "EDAM operation (no superclasses)": [ - "Taxonomic classification", - "Expression analysis", - "Cross-assembly" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbial ecology", - "Metagenomic sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "red", - "Galaxy tool ids": [ - "red" - ], - "Description": "Red (REpeat Detector)", - "bio.tool id": "red", - "bio.tool ids": [ - "red" - ], - "biii": null, - "bio.tool name": "RED", - "bio.tool description": "This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.", - "EDAM operation": [ - "RNA-Seq analysis", - "Editing" - ], - "EDAM topic": [ - "RNA", - "Sequencing", - "Data visualisation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/BioinformaticsToolsmith/Red", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "red", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/red", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/red", - "Galaxy wrapper version": "2018.09.10", - "Conda id": "red", - "Conda version": "2018.09.10", - "EDAM operation (no superclasses)": [ - "RNA-Seq analysis", - "Editing" - ], - "EDAM topic (no superclasses)": [ - "RNA", - "Sequencing", - "Data visualisation" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "repeatmasker", - "Galaxy tool ids": [ - "repeatmasker_wrapper" - ], - "Description": "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", - "bio.tool id": "repeatmasker", - "bio.tool ids": [ - "repeatmasker" - ], - "biii": null, - "bio.tool name": "RepeatMasker", - "bio.tool description": "A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).", - "EDAM operation": [ - "Genome annotation" - ], - "EDAM topic": [ - "Sequence analysis", - "Sequence composition, complexity and repeats" - ], - "Status": "Up-to-date", - "Source": "http://www.repeatmasker.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "repeat_masker", - "Galaxy wrapper owner": "bgruening", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker", - "Galaxy wrapper version": "4.1.5", - "Conda id": "repeatmasker", - "Conda version": "4.1.5", - "EDAM operation (no superclasses)": [ - "Genome annotation" - ], - "EDAM topic (no superclasses)": [ - "Sequence composition, complexity and repeats" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "repeatmodeler", - "Galaxy tool ids": [ - "repeatmodeler" - ], - "Description": "RepeatModeler - Model repetitive DNA", - "bio.tool id": "repeatmodeler", - "bio.tool ids": [ - "repeatmodeler" - ], - "biii": null, - "bio.tool name": "RepeatModeler", - "bio.tool description": "De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.", - "EDAM operation": [ - "Repeat sequence detection" - ], - "EDAM topic": [ - "Sequence composition, complexity and repeats", - "Sequence composition, complexity and repeats" - ], - "Status": "To update", - "Source": "https://www.repeatmasker.org/RepeatModeler/", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "repeatmodeler", - "Galaxy wrapper owner": "csbl", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler", - "Galaxy wrapper version": "2.0.5", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Repeat sequence detection" - ], - "EDAM topic (no superclasses)": [ - "Sequence composition, complexity and repeats", - "Sequence composition, complexity and repeats" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "repmatch_gff3", - "Galaxy tool ids": [ - "repmatch_gff3" - ], - "Description": "Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "repmatch_gff3", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3", - "Galaxy wrapper version": null, - "Conda id": "matplotlib", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "reshape2", - "Galaxy tool ids": [ - "cast", - "melt" - ], - "Description": "Flexibly restructure and aggregate data using just the two functions melt and dcast", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cran.r-project.org/web/packages/reshape2/index.html", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2", - "Galaxy wrapper version": "1.4.2", - "Conda id": "r-reshape2", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "resize_coordinate_window", - "Galaxy tool ids": [ - "resize_coordinate_window" - ], - "Description": "Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Genomic Interval Operations" - ], - "ToolShed id": "resize_coordinate_window", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window", - "Galaxy wrapper version": "1.0.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "revoluzer", - "Galaxy tool ids": [ - "revoluzer_crex", - "revoluzer_distmat" - ], - "Description": "revoluzer wrappers", - "bio.tool id": "revoluzer", - "bio.tool ids": [ - "revoluzer" - ], - "biii": null, - "bio.tool name": "revoluzer", - "bio.tool description": "Various tools for genome rearrangement analysis. CREx, TreeREx, etc", - "EDAM operation": [ - "Structural variation detection" - ], - "EDAM topic": [ - "Molecular evolution", - "Phylogeny" - ], - "Status": "Up-to-date", - "Source": "https://gitlab.com/Bernt/revoluzer/", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "revoluzer", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer", - "Galaxy wrapper version": "0.1.6", - "Conda id": "revoluzer", - "Conda version": "0.1.6", - "EDAM operation (no superclasses)": [ - "Structural variation detection" - ], - "EDAM topic (no superclasses)": [ - "Molecular evolution", - "Phylogeny" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rgcca", - "Galaxy tool ids": [ - "rgcca" - ], - "Description": "multi-block analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/rgcca-factory/RGCCA", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "rgcca", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca", - "Galaxy wrapper version": "3.0.2", - "Conda id": "rgccacmd", - "Conda version": "3.0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rgrnastar", - "Galaxy tool ids": [ - "rna_star", - "rna_starsolo" - ], - "Description": "RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper", - "bio.tool id": "star", - "bio.tool ids": [ - "star" - ], - "biii": null, - "bio.tool name": "STAR", - "bio.tool description": "Ultrafast universal RNA-seq data aligner", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "RNA-Seq", - "Transcriptomics" - ], - "Status": "To update", - "Source": "https://github.com/alexdobin/STAR", - "ToolShed categories": [ - "Next Gen Mappers", - "Transcriptomics" - ], - "ToolShed id": "rgrnastar", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar", - "Galaxy wrapper version": "2.7.11a", - "Conda id": "star", - "Conda version": "2.7.11b", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Transcriptomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "ribowaltz", - "Galaxy tool ids": [ - "ribowaltz_process", - "ribowaltz_plot" - ], - "Description": "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data", - "bio.tool id": "riboWaltz", - "bio.tool ids": [ - "riboWaltz" - ], - "biii": null, - "bio.tool name": "riboWaltz", - "bio.tool description": "riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.", - "EDAM operation": [], - "EDAM topic": [ - "Computational biology" - ], - "Status": "To update", - "Source": "https://github.com/LabTranslationalArchitectomics/riboWaltz", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz", - "Galaxy wrapper version": "1.2.0", - "Conda id": "ribowaltz", - "Conda version": "2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Computational biology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rnaquast", - "Galaxy tool ids": [ - "rna_quast" - ], - "Description": "rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.", - "bio.tool id": "rnaQUAST", - "bio.tool ids": [ - "rnaQUAST" - ], - "biii": null, - "bio.tool name": "rnaQUAST", - "bio.tool description": "Quality assessment tool for de novo transcriptome assemblies.", - "EDAM operation": [ - "De-novo assembly", - "Transcriptome assembly", - "Sequence assembly validation" - ], - "EDAM topic": [ - "Sequence assembly", - "Transcriptomics", - "RNA-seq" - ], - "Status": "Up-to-date", - "Source": "https://github.com/ablab/rnaquast", - "ToolShed categories": [ - "Assembly", - "RNA" - ], - "ToolShed id": "rnaquast", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://git.ufz.de/lehmanju/rnaquast", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast", - "Galaxy wrapper version": "2.2.3", - "Conda id": "rnaquast", - "Conda version": "2.2.3", - "EDAM operation (no superclasses)": [ - "De-novo assembly", - "Transcriptome assembly", - "Sequence assembly validation" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Transcriptomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "roary", - "Galaxy tool ids": [ - "roary" - ], - "Description": "Roary the pangenome pipeline", - "bio.tool id": "roary", - "bio.tool ids": [ - "roary" - ], - "biii": null, - "bio.tool name": "Roary", - "bio.tool description": "A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "DNA", - "Genomics", - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://sanger-pathogens.github.io/Roary/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "roary", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary", - "Galaxy wrapper version": "3.13.0", - "Conda id": "roary", - "Conda version": "3.13.0", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "DNA", - "Genomics", - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rp2biosensor", - "Galaxy tool ids": [ - "rp2biosensor" - ], - "Description": "Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/rp2biosensor", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rp2biosensor", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor", - "Galaxy wrapper version": "3.2.1", - "Conda id": "rp2biosensor", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rp2paths", - "Galaxy tool ids": [ - "rp2paths" - ], - "Description": "Enumerate and seperate the different pathways generated by RetroPath2.0", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/rp2paths", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rp2paths", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths", - "Galaxy wrapper version": "1.5.1", - "Conda id": "rp2paths", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rpbasicdesign", - "Galaxy tool ids": [ - "rpbasicdesign" - ], - "Description": "Extracting enzyme IDs from rpSBML files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/rpbasicdesign", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rpbasicdesign", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign", - "Galaxy wrapper version": "1.2.2", - "Conda id": "rpbasicdesign", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rpfba", - "Galaxy tool ids": [ - "rpfba" - ], - "Description": "Perform FBA for the RetroPath2.0 heterologous pathways", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/rptools/releases", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rpfba", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba", - "Galaxy wrapper version": "5.12.3", - "Conda id": "rptools", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rptools", - "Galaxy tool ids": [ - "rptools_rpextractsink", - "rptools_rpfba", - "rptools_rpranker", - "rptools_rpreport", - "rptools_rpviz" - ], - "Description": "Suite of tools that work on rpSBML format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/rptools", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rptools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools", - "Galaxy wrapper version": "5.13.1", - "Conda id": "rptools", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rrparser", - "Galaxy tool ids": [ - "rrparser" - ], - "Description": "Reaction Rules Parser", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/RRParser", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "rrparser", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser", - "Galaxy wrapper version": "2.5.2", - "Conda id": "rrparser", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rseqc", - "Galaxy tool ids": [ - "rseqc_FPKM_count", - "rseqc_RNA_fragment_size", - "rseqc_RPKM_saturation", - "rseqc_bam2wig", - "rseqc_bam_stat", - "rseqc_clipping_profile", - "rseqc_deletion_profile", - "rseqc_geneBody_coverage", - "rseqc_geneBody_coverage2", - "rseqc_infer_experiment", - "rseqc_inner_distance", - "rseqc_insertion_profile", - "rseqc_junction_annotation", - "rseqc_junction_saturation", - "rseqc_mismatch_profile", - "rseqc_read_GC", - "rseqc_read_NVC", - "rseqc_read_distribution", - "rseqc_read_duplication", - "rseqc_read_hexamer", - "rseqc_read_quality", - "rseqc_tin" - ], - "Description": "an RNA-seq quality control package", - "bio.tool id": "rseqc", - "bio.tool ids": [ - "rseqc" - ], - "biii": null, - "bio.tool name": "RSeQC", - "bio.tool description": "Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.", - "EDAM operation": [ - "Data handling" - ], - "EDAM topic": [ - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://code.google.com/p/rseqc/", - "ToolShed categories": [ - "Convert Formats", - "Sequence Analysis", - "RNA", - "Transcriptomics", - "Visualization" - ], - "ToolShed id": "rseqc", - "Galaxy wrapper owner": "nilesh", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc", - "Galaxy wrapper version": "5.0.3", - "Conda id": "rseqc", - "Conda version": "5.0.3", - "EDAM operation (no superclasses)": [ - "Data handling" - ], - "EDAM topic (no superclasses)": [ - "Sequencing" - ], - "Available on UseGalaxy.org": 22, - "Available on UseGalaxy.org.au": 22, - "Available on UseGalaxy.eu": 22, - "Available on UseGalaxy.org.fr": 22 - }, - { - "Galaxy wrapper id": "ruvseq", - "Galaxy tool ids": [ - "ruvseq" - ], - "Description": "Remove Unwanted Variation from RNA-Seq Data", - "bio.tool id": "ruvseq", - "bio.tool ids": [ - "ruvseq" - ], - "biii": null, - "bio.tool name": "RUVSeq", - "bio.tool description": "This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.", - "EDAM operation": [ - "Differential gene expression analysis" - ], - "EDAM topic": [ - "Gene expression", - "RNA-seq" - ], - "Status": "To update", - "Source": "https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "ruvseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq", - "Galaxy wrapper version": "1.26.0", - "Conda id": "bioconductor-ruvseq", - "Conda version": "1.36.0", - "EDAM operation (no superclasses)": [ - "Differential gene expression analysis" - ], - "EDAM topic (no superclasses)": [ - "Gene expression" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "salsa2", - "Galaxy tool ids": [ - "salsa" - ], - "Description": "A tool to scaffold long read assemblies with Hi-C", - "bio.tool id": "SALSA", - "bio.tool ids": [ - "SALSA" - ], - "biii": null, - "bio.tool name": "SALSA", - "bio.tool description": "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch", - "EDAM operation": [ - "Genome assembly", - "De-novo assembly", - "Scaffolding" - ], - "EDAM topic": [ - "Sequence assembly", - "DNA binding sites", - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/SALSA", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "salsa", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2", - "Galaxy wrapper version": "2.3", - "Conda id": "salsa2", - "Conda version": "2.3", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "De-novo assembly", - "Scaffolding" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "DNA binding sites", - "Mapping" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "samblaster", - "Galaxy tool ids": [ - "samblaster" - ], - "Description": "samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files", - "bio.tool id": "samblaster", - "bio.tool ids": [ - "samblaster" - ], - "biii": null, - "bio.tool name": "SAMBLASTER", - "bio.tool description": "A tool to mark duplicates and extract discordant and split reads from SAM files.", - "EDAM operation": [ - "Split read mapping" - ], - "EDAM topic": [ - "DNA", - "Sequencing", - "Mapping" - ], - "Status": "To update", - "Source": "https://github.com/GregoryFaust/samblaster", - "ToolShed categories": [ - "SAM", - "Fastq Manipulation", - "Variant Analysis" - ], - "ToolShed id": "samblaster", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster", - "Galaxy wrapper version": "0.1.24", - "Conda id": "samblaster", - "Conda version": "0.1.26", - "EDAM operation (no superclasses)": [ - "Split read mapping" - ], - "EDAM topic (no superclasses)": [ - "DNA", - "Sequencing", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sansa", - "Galaxy tool ids": [ - "sansa_annotate" - ], - "Description": "Sansa is a tool for structural variant annotation.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/dellytools/sansa", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "sansa", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa", - "Galaxy wrapper version": "0.2.1", - "Conda id": "sansa", - "Conda version": "0.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sarscov2formatter", - "Galaxy tool ids": [ - "sarscov2formatter" - ], - "Description": "sarscov2formatter custom script", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/nickeener/sarscov2formatter", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sarscov2formatter", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter", - "Galaxy wrapper version": "1.0", - "Conda id": "sarscov2formatter", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sarscov2summary", - "Galaxy tool ids": [ - "sarscov2summary" - ], - "Description": "sarscov2summary custom script", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nickeener/sarscov2summary", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sarscov2summary", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary", - "Galaxy wrapper version": "0.1", - "Conda id": "sarscov2summary", - "Conda version": "0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sbml2sbol", - "Galaxy tool ids": [ - "sbml2sbol" - ], - "Description": "Convert SBML to SBOL format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/neilswainston/SbmlToSbol", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "sbml2sbol", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol", - "Galaxy wrapper version": "0.1.13", - "Conda id": "sbml2sbol", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scanpy", - "Galaxy tool ids": [ - "scanpy_cluster_reduce_dimension", - "scanpy_filter", - "scanpy_inspect", - "scanpy_normalize", - "scanpy_plot", - "scanpy_remove_confounders" - ], - "Description": "Scanpy – Single-Cell Analysis in Python", - "bio.tool id": "scanpy", - "bio.tool ids": [ - "scanpy" - ], - "biii": null, - "bio.tool name": "SCANPY", - "bio.tool description": "Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.", - "EDAM operation": [ - "Differential gene expression analysis" - ], - "EDAM topic": [ - "Gene expression", - "Cell biology", - "Genetics" - ], - "Status": "To update", - "Source": "https://scanpy.readthedocs.io", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "scanpy", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy", - "Galaxy wrapper version": "1.9.6", - "Conda id": "scanpy", - "Conda version": "1.7.2", - "EDAM operation (no superclasses)": [ - "Differential gene expression analysis" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "Cell biology", - "Genetics" - ], - "Available on UseGalaxy.org": 6, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scater", - "Galaxy tool ids": [ - "scater_create_qcmetric_ready_sce", - "scater_filter", - "scater_plot_dist_scatter", - "scater_plot_pca", - "scater_plot_tsne" - ], - "Description": "Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.", - "bio.tool id": "scater", - "bio.tool ids": [ - "scater" - ], - "biii": null, - "bio.tool name": "scater", - "bio.tool description": "Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.", - "EDAM operation": [ - "Read pre-processing", - "Sequencing quality control", - "Sequence visualisation" - ], - "EDAM topic": [ - "RNA-seq", - "Quality affairs", - "Molecular genetics" - ], - "Status": "To update", - "Source": "http://bioconductor.org/packages/scater/", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Visualization" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater", - "Galaxy wrapper version": "1.22.0", - "Conda id": "bioconductor-scater", - "Conda version": "1.30.1", - "EDAM operation (no superclasses)": [ - "Read pre-processing", - "Sequence visualisation" - ], - "EDAM topic (no superclasses)": [ - "Quality affairs", - "Molecular genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sceasy", - "Galaxy tool ids": [ - "sceasy_convert" - ], - "Description": "Converter between difference single-cell formats", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/cellgeni/sceasy/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "sceasy_convert", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy", - "Galaxy wrapper version": "0.0.7", - "Conda id": "r-sceasy", - "Conda version": "0.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "schicexplorer", - "Galaxy tool ids": [ - "schicexplorer_schicadjustmatrix", - "schicexplorer_schiccluster", - "schicexplorer_schicclustercompartments", - "schicexplorer_schicclusterminhash", - "schicexplorer_schicclustersvl", - "schicexplorer_schicconsensusmatrices", - "schicexplorer_schiccorrectmatrices", - "schicexplorer_schiccreatebulkmatrix", - "schicexplorer_schicdemultiplex", - "schicexplorer_schicinfo", - "schicexplorer_schicmergematrixbins", - "schicexplorer_schicmergetoscool", - "schicexplorer_schicnormalize", - "schicexplorer_schicplotclusterprofiles", - "schicexplorer_schicplotconsensusmatrices", - "schicexplorer_schicqualitycontrol" - ], - "Description": "scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/joachimwolff/schicexplorer", - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics", - "Visualization" - ], - "ToolShed id": "schicexplorer", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer", - "Galaxy wrapper version": "4", - "Conda id": "schicexplorer", - "Conda version": "7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 16, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scikit-bio", - "Galaxy tool ids": [ - "scikit_bio_diversity_beta_diversity" - ], - "Description": "scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://scikit-bio.org/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "scikit_bio", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio", - "Galaxy wrapper version": "0.4.2", - "Conda id": "scikit-bio", - "Conda version": "0.4.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scoary", - "Galaxy tool ids": [ - "scoary" - ], - "Description": "Scoary calculates the assocations between all genes in the accessory genome and the traits.", - "bio.tool id": "scoary", - "bio.tool ids": [ - "scoary" - ], - "biii": null, - "bio.tool name": "Scoary", - "bio.tool description": "Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.", - "EDAM operation": [ - "Analysis" - ], - "EDAM topic": [ - "Genotype and phenotype", - "Model organisms", - "GWAS study", - "Functional genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/AdmiralenOla/Scoary", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "scoary", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary", - "Galaxy wrapper version": "1.6.16", - "Conda id": "scoary", - "Conda version": "1.6.16", - "EDAM operation (no superclasses)": [ - "Analysis" - ], - "EDAM topic (no superclasses)": [ - "Genotype and phenotype", - "Model organisms", - "GWAS study", - "Functional genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scpipe", - "Galaxy tool ids": [ - "scpipe" - ], - "Description": "A flexible preprocessing pipeline for single-cell RNA-sequencing data", - "bio.tool id": "scpipe", - "bio.tool ids": [ - "scpipe" - ], - "biii": null, - "bio.tool name": "scPipe", - "bio.tool description": "A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.", - "EDAM operation": [ - "Genome annotation", - "Validation", - "Alignment", - "Visualisation" - ], - "EDAM topic": [ - "Gene expression", - "RNA-Seq", - "Sequencing" - ], - "Status": "To update", - "Source": "http://bioconductor.org/packages/release/bioc/html/scPipe.html", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "scpipe", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe", - "Galaxy wrapper version": "1.0.0+galaxy2", - "Conda id": "bioconductor-scpipe", - "Conda version": "2.2.0", - "EDAM operation (no superclasses)": [ - "Genome annotation", - "Validation", - "Alignment", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "RNA-Seq" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seacr", - "Galaxy tool ids": [ - "seacr" - ], - "Description": "SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/FredHutch/SEACR", - "ToolShed categories": [ - "Epigenetics", - "ChIP-seq" - ], - "ToolShed id": "seacr", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr", - "Galaxy wrapper version": "1.3", - "Conda id": "seacr", - "Conda version": "1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "selenzy_wrapper", - "Galaxy tool ids": [ - "selenzy_wrapper" - ], - "Description": "Performs enzyme selection from a reaction query.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/brsynth/selenzy-wrapper", - "ToolShed categories": [ - "Synthetic Biology" - ], - "ToolShed id": "selenzy_wrapper", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper", - "Galaxy wrapper version": "0.3.0", - "Conda id": "selenzy_wrapper", - "Conda version": "0.3.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "semibin", - "Galaxy tool ids": [ - "semibin_bin", - "semibin_concatenate_fasta", - "semibin_generate_cannot_links", - "semibin_generate_sequence_features", - "semibin", - "semibin_train" - ], - "Description": "SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks", - "bio.tool id": "semibin", - "bio.tool ids": [ - "semibin" - ], - "biii": null, - "bio.tool name": "SemiBin", - "bio.tool description": "Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.", - "EDAM operation": [ - "Sequence assembly", - "Read binning" - ], - "EDAM topic": [ - "Metagenomics", - "Machine learning", - "Microbial ecology", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://semibin.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "semibin", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin", - "Galaxy wrapper version": "2.0.2", - "Conda id": "semibin", - "Conda version": "2.1.0", - "EDAM operation (no superclasses)": [ - "Sequence assembly", - "Read binning" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Machine learning", - "Microbial ecology", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "seq2hla", - "Galaxy tool ids": [ - "seq2hla" - ], - "Description": "Precision HLA typing and expression from RNAseq data", - "bio.tool id": "seq2hla", - "bio.tool ids": [ - "seq2hla" - ], - "biii": null, - "bio.tool name": "Seq2HLA", - "bio.tool description": "seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.", - "EDAM operation": [ - "Read mapping", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Transcriptomics", - "Mapping" - ], - "Status": "Up-to-date", - "Source": "https://github.com/TRON-Bioinformatics/seq2HLA", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seq2hla", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla", - "Galaxy wrapper version": "2.3", - "Conda id": "seq2hla", - "Conda version": "2.3", - "EDAM operation (no superclasses)": [ - "Read mapping", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Mapping" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seqcomplexity", - "Galaxy tool ids": [ - "seqcomplexity" - ], - "Description": "Sequence complexity for raw reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/stevenweaver/seqcomplexity", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity", - "Galaxy wrapper version": "0.1.2", - "Conda id": "seqcomplexity", - "Conda version": "0.1.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seqkit", - "Galaxy tool ids": [ - "seqkit_fx2tab", - "seqkit_locate", - "seqkit_sort", - "seqkit_stats", - "seqkit_translate" - ], - "Description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", - "bio.tool id": "seqkit", - "bio.tool ids": [ - "seqkit" - ], - "biii": null, - "bio.tool name": "seqkit", - "bio.tool description": "FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.", - "EDAM operation": [ - "DNA transcription", - "Sequence trimming", - "DNA translation", - "Sequence conversion" - ], - "EDAM topic": [ - "Database management", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://bioinf.shenwei.me/seqkit/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seqkit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit", - "Galaxy wrapper version": "2.8.2", - "Conda id": "seqkit", - "Conda version": "2.8.2", - "EDAM operation (no superclasses)": [ - "DNA transcription", - "Sequence trimming", - "DNA translation" - ], - "EDAM topic (no superclasses)": [ - "Database management", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "seqprep", - "Galaxy tool ids": [ - "seqprep" - ], - "Description": "Tool for merging paired-end Illumina reads and trimming adapters.", - "bio.tool id": "seqprep", - "bio.tool ids": [ - "seqprep" - ], - "biii": null, - "bio.tool name": "SeqPrep", - "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", - "EDAM operation": [ - "Nucleic acid design" - ], - "EDAM topic": [ - "Genomics", - "Sequence assembly", - "Sequencing", - "Probes and primers" - ], - "Status": "Up-to-date", - "Source": "https://github.com/jstjohn/SeqPrep", - "ToolShed categories": [ - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "seqprep", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep", - "Galaxy wrapper version": "1.3.2", - "Conda id": "seqprep", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [ - "Nucleic acid design" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly", - "Sequencing", - "Probes and primers" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seqsero2", - "Galaxy tool ids": [ - "seqsero2" - ], - "Description": "Salmonella serotype prediction from genome sequencing data", - "bio.tool id": "seqsero2", - "bio.tool ids": [ - "seqsero2" - ], - "biii": null, - "bio.tool name": "SeqSero2", - "bio.tool description": "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)", - "EDAM operation": [ - "Genome indexing", - "Antimicrobial resistance prediction", - "Genome alignment" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Sequence assembly", - "Genomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/denglab/SeqSero2", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seqsero2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", - "Galaxy wrapper version": "1.3.1", - "Conda id": "seqsero2", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [ - "Genome indexing", - "Antimicrobial resistance prediction", - "Genome alignment" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Sequence assembly", - "Genomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seqtk", - "Galaxy tool ids": [ - "seqtk_comp", - "seqtk_cutN", - "seqtk_dropse", - "seqtk_fqchk", - "seqtk_hety", - "seqtk_listhet", - "seqtk_mergefa", - "seqtk_mergepe", - "seqtk_mutfa", - "seqtk_randbase", - "seqtk_sample", - "seqtk_seq", - "seqtk_subseq", - "seqtk_telo", - "seqtk_trimfq" - ], - "Description": "Toolkit for processing sequences in FASTA/Q formats", - "bio.tool id": "seqtk", - "bio.tool ids": [ - "seqtk" - ], - "biii": null, - "bio.tool name": "seqtk", - "bio.tool description": "A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.", - "EDAM operation": [ - "Data handling", - "Sequence file editing" - ], - "EDAM topic": [ - "Data management" - ], - "Status": "Up-to-date", - "Source": "https://github.com/lh3/seqtk", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "seqtk", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk", - "Galaxy wrapper version": "1.4", - "Conda id": "seqtk", - "Conda version": "1.4", - "EDAM operation (no superclasses)": [ - "Data handling", - "Sequence file editing" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 15, - "Available on UseGalaxy.org.au": 15, - "Available on UseGalaxy.eu": 15, - "Available on UseGalaxy.org.fr": 15 - }, - { - "Galaxy wrapper id": "seqwish", - "Galaxy tool ids": [ - "seqwish" - ], - "Description": "Alignment to variation graph inducer", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/seqwish", - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish", - "Galaxy wrapper version": "0.7.5", - "Conda id": "seqwish", - "Conda version": "0.7.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seurat", - "Galaxy tool ids": [ - "seurat" - ], - "Description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/satijalab/seurat", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "seurat", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat", - "Galaxy wrapper version": "4.3.0.1", - "Conda id": "r-seurat", - "Conda version": "3.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "shasta", - "Galaxy tool ids": [ - "shasta" - ], - "Description": "Fast de novo assembly of long read sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/chanzuckerberg/shasta", - "ToolShed categories": [ - "Assembly", - "Nanopore" - ], - "ToolShed id": "shasta", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta", - "Galaxy wrapper version": "0.6.0", - "Conda id": "shasta", - "Conda version": "0.12.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "shorah", - "Galaxy tool ids": [ - "shorah_amplicon" - ], - "Description": "Reconstruct haplotypes using ShoRAH in amplicon mode", - "bio.tool id": "shorah", - "bio.tool ids": [ - "shorah" - ], - "biii": null, - "bio.tool name": "ShoRAH", - "bio.tool description": "Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.", - "EDAM operation": [ - "Haplotype mapping", - "Variant calling" - ], - "EDAM topic": [ - "Metagenomics", - "Sequencing", - "Genetics" - ], - "Status": "To update", - "Source": "https://github.com/cbg-ethz/shorah/blob/master/README.md", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "shorah_amplicon", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah", - "Galaxy wrapper version": "1.1.3", - "Conda id": "shorah", - "Conda version": "1.99.2", - "EDAM operation (no superclasses)": [ - "Haplotype mapping", - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequencing", - "Genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "shovill", - "Galaxy tool ids": [ - "shovill" - ], - "Description": "Faster de novo assembly pipeline based around Spades", - "bio.tool id": "shovill", - "bio.tool ids": [ - "shovill" - ], - "biii": null, - "bio.tool name": "shovill", - "bio.tool description": "Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Genomics", - "Microbiology", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/tseemann/shovill", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "shovill", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", - "Galaxy wrapper version": "1.1.0", - "Conda id": "shovill", - "Conda version": "1.1.0", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Microbiology", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "sickle", - "Galaxy tool ids": [ - "sickle" - ], - "Description": "A windowed adaptive trimming tool for FASTQ files using quality", - "bio.tool id": "sickle", - "bio.tool ids": [ - "sickle" - ], - "biii": null, - "bio.tool name": "sickle", - "bio.tool description": "A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.", - "EDAM operation": [ - "Sequence trimming" - ], - "EDAM topic": [ - "Data quality management" - ], - "Status": "To update", - "Source": "https://github.com/najoshi/sickle", - "ToolShed categories": [ - "Fastq Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "sickle", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle", - "Galaxy wrapper version": "1.33.2", - "Conda id": "sickle-trim", - "Conda version": "1.33", - "EDAM operation (no superclasses)": [ - "Sequence trimming" - ], - "EDAM topic (no superclasses)": [ - "Data quality management" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "simtext", - "Galaxy tool ids": [ - "abstracts_by_pmids", - "pmids_to_pubtator_matrix", - "pubmed_by_queries", - "text_to_wordmatrix" - ], - "Description": "A text mining framework for interactive analysis and visualization of similarities among biomedical entities.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/dlal-group/simtext", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "simtext", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/simtext", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext", - "Galaxy wrapper version": "0.0.2", - "Conda id": "r-argparse", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sina", - "Galaxy tool ids": [ - "sina" - ], - "Description": "SINA reference based multiple sequence alignment", - "bio.tool id": "sina", - "bio.tool ids": [ - "sina" - ], - "biii": null, - "bio.tool name": "SINA", - "bio.tool description": "Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment", - "EDAM operation": [ - "Sequence alignment analysis", - "Multiple sequence alignment", - "Taxonomic classification", - "Structure-based sequence alignment" - ], - "EDAM topic": [ - "Sequencing", - "RNA", - "Nucleic acid structure analysis", - "Taxonomy", - "Sequence analysis", - "Taxonomy" - ], - "Status": "Up-to-date", - "Source": "https://sina.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sina", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina", - "Galaxy wrapper version": "1.7.2", - "Conda id": "sina", - "Conda version": "1.7.2", - "EDAM operation (no superclasses)": [ - "Sequence alignment analysis", - "Multiple sequence alignment", - "Taxonomic classification", - "Structure-based sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "RNA", - "Nucleic acid structure analysis", - "Taxonomy", - "Sequence analysis", - "Taxonomy" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sinto", - "Galaxy tool ids": [ - "sinto_barcode", - "sinto_fragments" - ], - "Description": "Sinto single-cell analysis tools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/timoast/sinto", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto", - "Galaxy wrapper version": "0.9.0", - "Conda id": "sinto", - "Conda version": "0.10.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "slamdunk", - "Galaxy tool ids": [ - "alleyoop", - "slamdunk" - ], - "Description": "Slamdunk maps and quantifies SLAMseq reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://t-neumann.github.io/slamdunk", - "ToolShed categories": [ - "RNA", - "Transcriptomics", - "Sequence Analysis", - "Next Gen Mappers" - ], - "ToolShed id": "slamdunk", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk", - "Galaxy wrapper version": "0.4.3", - "Conda id": "slamdunk", - "Conda version": "0.4.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sleuth", - "Galaxy tool ids": [ - "sleuth" - ], - "Description": "Sleuth is a program for differential analysis of RNA-Seq data.", - "bio.tool id": "sleuth", - "bio.tool ids": [ - "sleuth" - ], - "biii": null, - "bio.tool name": "sleuth", - "bio.tool description": "A statistical model and software application for RNA-seq differential expression analysis.", - "EDAM operation": [ - "Expression data visualisation", - "Differential gene expression analysis", - "Gene expression profiling", - "Statistical calculation" - ], - "EDAM topic": [ - "RNA-seq", - "Gene expression", - "Statistics and probability" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pachterlab/sleuth", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "sleuth", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth", - "Galaxy wrapper version": "0.30.1", - "Conda id": "r-sleuth", - "Conda version": "0.30.1", - "EDAM operation (no superclasses)": [ - "Expression data visualisation", - "Differential gene expression analysis", - "Gene expression profiling", - "Statistical calculation" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smallgenomeutilities", - "Galaxy tool ids": [ - "smgu_frameshift_deletions_checks" - ], - "Description": "Set of utilities for manipulating small viral genome data.", - "bio.tool id": "v-pipe", - "bio.tool ids": [ - "v-pipe" - ], - "biii": null, - "bio.tool name": "V-pipe", - "bio.tool description": "Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.", - "EDAM operation": [ - "Read pre-processing", - "Sequence alignment", - "Genetic variation analysis" - ], - "EDAM topic": [ - "Genomics", - "Population genetics", - "Workflows", - "Virology", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/cbg-ethz/smallgenomeutilities", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "smallgenomeutilities", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities", - "Galaxy wrapper version": "0.4.1", - "Conda id": "smallgenomeutilities", - "Conda version": "0.4.1", - "EDAM operation (no superclasses)": [ - "Read pre-processing", - "Sequence alignment", - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Population genetics", - "Workflows", - "Virology", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smudgeplot", - "Galaxy tool ids": [ - "smudgeplot" - ], - "Description": "Inference of ploidy and heterozygosity structure using whole genome sequencing", - "bio.tool id": "smudgeplots", - "bio.tool ids": [ - "smudgeplots" - ], - "biii": null, - "bio.tool name": "Smudgeplots", - "bio.tool description": "Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568", - "EDAM operation": [ - "Sequence trimming", - "Genotyping", - "k-mer counting" - ], - "EDAM topic": [ - "Sequence assembly", - "Genetic variation", - "Mathematics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/KamilSJaron/smudgeplot", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "smudgeplot", - "Galaxy wrapper owner": "galaxy-australia", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot", - "Galaxy wrapper version": "0.2.5", - "Conda id": "smudgeplot", - "Conda version": "0.2.5", - "EDAM operation (no superclasses)": [ - "Sequence trimming", - "Genotyping", - "k-mer counting" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly", - "Genetic variation", - "Mathematics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snap", - "Galaxy tool ids": [ - "snap", - "snap_training" - ], - "Description": "SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.", - "bio.tool id": "snap", - "bio.tool ids": [ - "snap" - ], - "biii": null, - "bio.tool name": "SNAP", - "bio.tool description": "The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.", - "EDAM operation": [ - "Gene prediction" - ], - "EDAM topic": [ - "DNA", - "DNA polymorphism", - "Genetics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/KorfLab/SNAP", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "snap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap", - "Galaxy wrapper version": "2013_11_29", - "Conda id": "snap", - "Conda version": "2013_11_29", - "EDAM operation (no superclasses)": [ - "Gene prediction" - ], - "EDAM topic (no superclasses)": [ - "DNA polymorphism", - "Genetics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snapatac2", - "Galaxy tool ids": [ - "snapatac2_clustering", - "snapatac2_peaks_and_motif", - "snapatac2_plotting", - "snapatac2_preprocessing" - ], - "Description": "SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://kzhang.org/SnapATAC2/", - "ToolShed categories": [ - "Epigenetics", - "Sequence Analysis" - ], - "ToolShed id": "snapatac2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2", - "Galaxy wrapper version": "2.5.3", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sniffles", - "Galaxy tool ids": [ - "sniffles" - ], - "Description": "Galaxy wrapper for sniffles", - "bio.tool id": "sniffles", - "bio.tool ids": [ - "sniffles" - ], - "biii": null, - "bio.tool name": "Sniffles", - "bio.tool description": "An algorithm for structural variation detection from third generation sequencing alignment.", - "EDAM operation": [ - "Sequence analysis", - "Structural variation detection" - ], - "EDAM topic": [ - "DNA structural variation", - "Sequencing" - ], - "Status": "To update", - "Source": "https://github.com/fritzsedlazeck/Sniffles", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sniffles", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles", - "Galaxy wrapper version": "1.0.12", - "Conda id": "sniffles", - "Conda version": "2.3.3", - "EDAM operation (no superclasses)": [ - "Sequence analysis", - "Structural variation detection" - ], - "EDAM topic (no superclasses)": [ - "Sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "snipit", - "Galaxy tool ids": [ - "snipit" - ], - "Description": "Summarise snps relative to a reference sequence", - "bio.tool id": "snipit", - "bio.tool ids": [ - "snipit" - ], - "biii": null, - "bio.tool name": "snipit", - "bio.tool description": "Summarise snps relative to a reference sequence", - "EDAM operation": [ - "Base position variability plotting" - ], - "EDAM topic": [ - "Virology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/aineniamh/snipit", - "ToolShed categories": [ - "Variant Analysis", - "Sequence Analysis" - ], - "ToolShed id": "snipit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit", - "Galaxy wrapper version": "1.2", - "Conda id": "snipit", - "Conda version": "1.2", - "EDAM operation (no superclasses)": [ - "Base position variability plotting" - ], - "EDAM topic (no superclasses)": [ - "Virology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snippy", - "Galaxy tool ids": [ - "snippy_core", - "snippy", - "snippy_clean_full_aln" - ], - "Description": "Contains the snippy tool for characterising microbial snps", - "bio.tool id": "snippy", - "bio.tool ids": [ - "snippy" - ], - "biii": null, - "bio.tool name": "snippy", - "bio.tool description": "Rapid haploid variant calling and core SNP phylogeny generation.", - "EDAM operation": [ - "Phylogenetic tree visualisation", - "Phylogenetic tree generation", - "Variant calling" - ], - "EDAM topic": [ - "Genomics", - "Model organisms", - "DNA polymorphism", - "Phylogenetics" - ], - "Status": "To update", - "Source": "https://github.com/tseemann/snippy", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "snippy", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy", - "Galaxy wrapper version": null, - "Conda id": "snippy", - "Conda version": "4.6.0", - "EDAM operation (no superclasses)": [ - "Phylogenetic tree visualisation", - "Variant calling" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Model organisms", - "DNA polymorphism", - "Phylogenetics" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "snp-dists", - "Galaxy tool ids": [ - "snp_dists" - ], - "Description": "Compute pairwise SNP distance matrix from a FASTA sequence alignment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/tseemann/snp-dists", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snp_dists", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists", - "Galaxy wrapper version": "0.8.2", - "Conda id": "snp-dists", - "Conda version": "0.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snp-sites", - "Galaxy tool ids": [ - "snp_sites" - ], - "Description": "Finds SNP sites from a multi-FASTA alignment file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/sanger-pathogens/snp-sites", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snp_sites", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites", - "Galaxy wrapper version": "2.5.1", - "Conda id": "snp-sites", - "Conda version": "2.5.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snpeff-covid19", - "Galaxy tool ids": [ - "snpeff_sars_cov_2" - ], - "Description": "SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox", - "bio.tool id": "snpeff", - "bio.tool ids": [ - "snpeff" - ], - "biii": null, - "bio.tool name": "snpEff", - "bio.tool description": "Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).", - "EDAM operation": [ - "SNP detection" - ], - "EDAM topic": [ - "DNA polymorphism", - "Genetic variation", - "Nucleic acid sites, features and motifs" - ], - "Status": "To update", - "Source": "http://snpeff.sourceforge.net/", - "ToolShed categories": [ - "Genome-Wide Association Study", - "Variant Analysis" - ], - "ToolShed id": "snpeff_sars_cov_2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "SNP detection" - ], - "EDAM topic (no superclasses)": [ - "DNA polymorphism", - "Nucleic acid sites, features and motifs" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "snpfreqplot", - "Galaxy tool ids": [ - "snpfreqplot" - ], - "Description": "Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snpfreqplot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot", - "Galaxy wrapper version": "1.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "socru", - "Galaxy tool ids": [ - "socru" - ], - "Description": "Order and orientation of complete bacterial genomes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/quadram-institute-bioscience/socru", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "socru", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru", - "Galaxy wrapper version": "2.1.7", - "Conda id": "socru", - "Conda version": "2.2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sonneityping", - "Galaxy tool ids": [ - "sonneityping" - ], - "Description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", - "bio.tool id": "sonneityping", - "bio.tool ids": [ - "sonneityping" - ], - "biii": null, - "bio.tool name": "sonneityping", - "bio.tool description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", - "EDAM operation": [ - "Antimicrobial resistance prediction", - "Variant calling", - "Genotyping" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Genotype and phenotype", - "Genetic variation", - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/katholt/sonneityping", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "sonneityping", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/katholt/sonneityping", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping", - "Galaxy wrapper version": "20210201", - "Conda id": "sonneityping", - "Conda version": "20210201", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction", - "Variant calling", - "Genotyping" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Genotype and phenotype", - "Genetic variation", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spades", - "Galaxy tool ids": [ - "spades_biosyntheticspades", - "spades_coronaspades", - "spades_metaplasmidspades", - "metaspades", - "spades_metaviralspades", - "spades_plasmidspades", - "rnaspades", - "spades_rnaviralspades", - "spades" - ], - "Description": "SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.", - "bio.tool id": "spades", - "bio.tool ids": [ - "rnaviralspades", - "metaspades", - "spades", - "metaplasmidspades", - "plasmidspades", - "biosyntheticspades", - "coronaspades", - "rnaspades", - "metaviralspades" - ], - "biii": null, - "bio.tool name": "SPAdes", - "bio.tool description": "St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.", - "EDAM operation": [ - "Genome assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/ablab/spades", - "ToolShed categories": [ - "Assembly", - "RNA", - "Metagenomics" - ], - "ToolShed id": "spades", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades", - "Galaxy wrapper version": "3.15.5", - "Conda id": "spades", - "Conda version": "4.0.0", - "EDAM operation (no superclasses)": [ - "Genome assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 9, - "Available on UseGalaxy.org.au": 9, - "Available on UseGalaxy.eu": 9, - "Available on UseGalaxy.org.fr": 9 - }, - { - "Galaxy wrapper id": "spaln", - "Galaxy tool ids": [ - "list_spaln_tables", - "spaln" - ], - "Description": "Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/", - "ToolShed categories": [ - "Sequence Analysis", - "Genome annotation" - ], - "ToolShed id": "spaln", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/ogotoh/spaln", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln", - "Galaxy wrapper version": "2.4.9", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spotyping", - "Galaxy tool ids": [ - "spotyping" - ], - "Description": "SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads", - "bio.tool id": "spotyping", - "bio.tool ids": [ - "spotyping" - ], - "biii": null, - "bio.tool name": "SpoTyping", - "bio.tool description": "Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.", - "EDAM operation": [ - "Variant pattern analysis" - ], - "EDAM topic": [ - "Microbiology", - "Sequencing", - "Sequence composition, complexity and repeats", - "Genetic variation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/xiaeryu/SpoTyping-v2.0", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "spotyping", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping", - "Galaxy wrapper version": "2.1", - "Conda id": "spotyping", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [ - "Variant pattern analysis" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Sequencing", - "Sequence composition, complexity and repeats", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spyboat", - "Galaxy tool ids": [ - "spyboat" - ], - "Description": "Wavelet analysis for 3d-image stacks", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://github.com/tensionhead/spyboat", - "ToolShed categories": [ - "Imaging", - "Graphics" - ], - "ToolShed id": "spyboat", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat", - "Galaxy wrapper version": "0.1.2", - "Conda id": "spyboat", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sra-tools", - "Galaxy tool ids": [ - "fasterq_dump", - "fastq_dump", - "sam_dump" - ], - "Description": "NCBI Sequence Read Archive toolkit utilities", - "bio.tool id": "sra-tools", - "bio.tool ids": [ - "sra-tools" - ], - "biii": null, - "bio.tool name": "SRA Software Toolkit", - "bio.tool description": "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.", - "EDAM operation": [ - "Data handling" - ], - "EDAM topic": [ - "DNA", - "Genomics", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "https://github.com/ncbi/sra-tools", - "ToolShed categories": [ - "Data Source", - "Fastq Manipulation" - ], - "ToolShed id": "sra_tools", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools", - "Galaxy wrapper version": "3.1.1", - "Conda id": "sra-tools", - "Conda version": "3.1.1", - "EDAM operation (no superclasses)": [ - "Data handling" - ], - "EDAM topic (no superclasses)": [ - "DNA", - "Genomics", - "Sequencing" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "srst2", - "Galaxy tool ids": [ - "srst2" - ], - "Description": "SRST2 Short Read Sequence Typing for Bacterial Pathogens", - "bio.tool id": "srst2", - "bio.tool ids": [ - "srst2" - ], - "biii": null, - "bio.tool name": "srst2", - "bio.tool description": "Short Read Sequence Typing for Bacterial Pathogens", - "EDAM operation": [ - "Multilocus sequence typing" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Public health and epidemiology" - ], - "Status": "To update", - "Source": "http://katholt.github.io/srst2/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "srst2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/katholt/srst2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2", - "Galaxy wrapper version": "0.2.0", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [ - "Multilocus sequence typing" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Public health and epidemiology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "stacks", - "Galaxy tool ids": [ - "stacks_assembleperead", - "stacks_clonefilter", - "stacks_cstacks", - "stacks_denovomap", - "stacks_genotypes", - "stacks_populations", - "stacks_procrad", - "stacks_pstacks", - "stacks_refmap", - "stacks_rxstacks", - "stacks_sstacks", - "stacks_stats", - "stacks_ustacks" - ], - "Description": "Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq", - "bio.tool id": "stacks", - "bio.tool ids": [ - "stacks" - ], - "biii": null, - "bio.tool name": "Stacks", - "bio.tool description": "Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.", - "EDAM operation": [ - "Data handling" - ], - "EDAM topic": [ - "Mapping", - "Population genetics" - ], - "Status": "To update", - "Source": "http://catchenlab.life.illinois.edu/stacks/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "stacks", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks", - "Galaxy wrapper version": null, - "Conda id": "stacks", - "Conda version": "2.65", - "EDAM operation (no superclasses)": [ - "Data handling" - ], - "EDAM topic (no superclasses)": [ - "Mapping", - "Population genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 13, - "Available on UseGalaxy.eu": 13, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "stacks2", - "Galaxy tool ids": [ - "stacks2_clonefilter", - "stacks2_cstacks", - "stacks2_denovomap", - "stacks2_gstacks", - "stacks2_kmerfilter", - "stacks2_populations", - "stacks2_procrad", - "stacks2_refmap", - "stacks2_shortreads", - "stacks2_sstacks", - "stacks2_tsv2bam", - "stacks2_ustacks" - ], - "Description": "Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://catchenlab.life.illinois.edu/stacks/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2", - "Galaxy wrapper version": "2.55", - "Conda id": "stacks", - "Conda version": "2.65", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 12, - "Available on UseGalaxy.eu": 12, - "Available on UseGalaxy.org.fr": 12 - }, - { - "Galaxy wrapper id": "star_fusion", - "Galaxy tool ids": [ - "star_fusion" - ], - "Description": "STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics" - ], - "ToolShed id": "star_fusion", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion", - "Galaxy wrapper version": "0.5.4-3+galaxy1", - "Conda id": "star-fusion", - "Conda version": "1.13.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "straindesign", - "Galaxy tool ids": [ - "straindesign_analyzing_model", - "straindesign_reduce_model", - "straindesign_simulate_deletion" - ], - "Description": "Toolbox to optimize biological model", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/brsynth/straindesign", - "ToolShed categories": [ - "Systems Biology", - "Synthetic Biology" - ], - "ToolShed id": "straindesign", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/brsynth/straindesign", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign", - "Galaxy wrapper version": "3.2.2", - "Conda id": "straindesign", - "Conda version": "3.2.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "strelka", - "Galaxy tool ids": [ - "strelka_germline", - "strelka_somatic" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/Illumina/strelka/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "strelka", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka", - "Galaxy wrapper version": "2.9.10", - "Conda id": "strelka", - "Conda version": "2.9.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "stringtie", - "Galaxy tool ids": [ - "stringtie", - "stringtie_merge" - ], - "Description": "StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.", - "bio.tool id": "stringtie", - "bio.tool ids": [ - "stringtie" - ], - "biii": null, - "bio.tool name": "StringTie", - "bio.tool description": "Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.", - "EDAM operation": [ - "Transcriptome assembly", - "RNA-Seq analysis" - ], - "EDAM topic": [ - "Transcriptomics", - "RNA-seq" - ], - "Status": "Up-to-date", - "Source": "http://ccb.jhu.edu/software/stringtie/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "stringtie", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie", - "Galaxy wrapper version": "2.2.3", - "Conda id": "stringtie", - "Conda version": "2.2.3", - "EDAM operation (no superclasses)": [ - "Transcriptome assembly", - "RNA-Seq analysis" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "structure", - "Galaxy tool ids": [ - "structure" - ], - "Description": "for using multi-locus genotype data to investigate population structure.", - "bio.tool id": "structure", - "bio.tool ids": [ - "structure" - ], - "biii": null, - "bio.tool name": "Structure", - "bio.tool description": "The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.", - "EDAM operation": [ - "Genetic variation analysis" - ], - "EDAM topic": [ - "Population genetics" - ], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Phylogenetics", - "Variant Analysis" - ], - "ToolShed id": "structure", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure", - "Galaxy wrapper version": "2.3.4", - "Conda id": "structure", - "Conda version": "2.3.4", - "EDAM operation (no superclasses)": [ - "Genetic variation analysis" - ], - "EDAM topic (no superclasses)": [ - "Population genetics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "structureharvester", - "Galaxy tool ids": [ - "structureharvester" - ], - "Description": "for parsing STRUCTURE outputs and for performing the Evanno method", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Phylogenetics", - "Variant Analysis" - ], - "ToolShed id": "structureharvester", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester", - "Galaxy wrapper version": "0.6.94", - "Conda id": "structureharvester", - "Conda version": "0.6.94", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "swift", - "Galaxy tool ids": [ - "swiftlink" - ], - "Description": "Parallel MCMC Linkage Analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/ajm/swiftlink", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "swiftlink", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift", - "Galaxy wrapper version": "1.0", - "Conda id": "swiftlink", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "syndiva", - "Galaxy tool ids": [ - "syndiva" - ], - "Description": "SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "syndiva", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva", - "Galaxy wrapper version": "1.0", - "Conda id": "clustalo", - "Conda version": "1.2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "table_compute", - "Galaxy tool ids": [ - "table_compute" - ], - "Description": "Perform general-purpose table operations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "table_compute", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute", - "Galaxy wrapper version": "1.2.4", - "Conda id": "pandas", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tag_pileup_frequency", - "Galaxy tool ids": [ - "tag_pileup_frequency" - ], - "Description": "Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup", - "ToolShed categories": [ - "Statistics", - "SAM", - "Genomic Interval Operations" - ], - "ToolShed id": "tag_pileup_frequency", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency", - "Galaxy wrapper version": "1.0.2", - "Conda id": "openjdk", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tasmanian_mismatch", - "Galaxy tool ids": [ - "tasmanian_mismatch" - ], - "Description": "Analysis of positional mismatches", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tasmanian_mismatch", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/nebiolabs/tasmanian-mismatch", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch", - "Galaxy wrapper version": "1.0.7", - "Conda id": "tasmanian-mismatch", - "Conda version": "1.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "taxonomy_filter_refseq", - "Galaxy tool ids": [ - "taxonomy_filter_refseq" - ], - "Description": "Filter RefSeq by taxonomy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/pvanheus/ncbitaxonomy", - "ToolShed categories": [ - "Sequence Analysis", - "Genome annotation" - ], - "ToolShed id": "taxonomy_filter_refseq", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq", - "Galaxy wrapper version": "0.3.0", - "Conda id": "rust-ncbitaxonomy", - "Conda version": "1.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "taxonomy_krona_chart", - "Galaxy tool ids": [ - "taxonomy_krona_chart" - ], - "Description": "Krona pie chart from taxonomic profile", - "bio.tool id": "krona", - "bio.tool ids": [ - "krona" - ], - "biii": null, - "bio.tool name": "Krona", - "bio.tool description": "Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).", - "EDAM operation": [ - "Visualisation" - ], - "EDAM topic": [ - "Metagenomics" - ], - "Status": "To update", - "Source": "http://sourceforge.net/projects/krona/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "taxonomy_krona_chart", - "Galaxy wrapper owner": "crs4", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart", - "Galaxy wrapper version": "2.7.1+galaxy0", - "Conda id": "krona", - "Conda version": "2.8.1", - "EDAM operation (no superclasses)": [ - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tb-profiler", - "Galaxy tool ids": [ - "tb_profiler_profile" - ], - "Description": "Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.", - "bio.tool id": "tb-profiler", - "bio.tool ids": [ - "tb-profiler" - ], - "biii": null, - "bio.tool name": "tb-profiler", - "bio.tool description": "A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).", - "EDAM operation": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/jodyphelan/TBProfiler", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tbprofiler", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler", - "Galaxy wrapper version": "6.2.1", - "Conda id": "tb-profiler", - "Conda version": "6.2.1", - "EDAM operation (no superclasses)": [ - "Antimicrobial resistance prediction" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tb_variant_filter", - "Galaxy tool ids": [ - "tb_variant_filter" - ], - "Description": "M. tuberculosis H37Rv VCF filter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/COMBAT-TB/tb_variant_filter", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "tb_variant_filter", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/COMBAT-TB/tb_variant_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter", - "Galaxy wrapper version": "0.4.0", - "Conda id": "tb_variant_filter", - "Conda version": "0.4.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tbl2gff3", - "Galaxy tool ids": [ - "tbl2gff3" - ], - "Description": "Table to GFF3", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3", - "ToolShed categories": [ - "Convert Formats", - "Sequence Analysis" - ], - "ToolShed id": "tbl2gff3", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3", - "Galaxy wrapper version": "1.2", - "Conda id": "bcbiogff", - "Conda version": "0.6.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tbvcfreport", - "Galaxy tool ids": [ - "tbvcfreport" - ], - "Description": "Generate HTML report from SnpEff M.tuberculosis VCF(s)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/COMBAT-TB/tbvcfreport", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "tbvcfreport", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport", - "Galaxy wrapper version": "1.0.0", - "Conda id": "tbvcfreport", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "te_finder", - "Galaxy tool ids": [ - "te_finder" - ], - "Description": "Transposable element insertions finder", - "bio.tool id": "tefinder", - "bio.tool ids": [ - "tefinder" - ], - "biii": null, - "bio.tool name": "TEfinder", - "bio.tool description": "A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.", - "EDAM operation": [ - "Genome indexing", - "Variant calling", - "PCR primer design" - ], - "EDAM topic": [ - "Sequencing", - "Mobile genetic elements", - "Workflows", - "Evolutionary biology", - "Genetic variation" - ], - "Status": "To update", - "Source": "https://github.com/VistaSohrab/TEfinder", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "te_finder", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder", - "Galaxy wrapper version": "1.0.1", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [ - "Genome indexing", - "Variant calling", - "PCR primer design" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Mobile genetic elements", - "Workflows", - "Evolutionary biology", - "Genetic variation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "telescope", - "Galaxy tool ids": [ - "telescope_assign" - ], - "Description": "Single locus resolution of Transposable ELEment expression.", - "bio.tool id": "Telescope-expression", - "bio.tool ids": [ - "Telescope-expression" - ], - "biii": null, - "bio.tool name": "Telescope", - "bio.tool description": "Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.", - "EDAM operation": [ - "Essential dynamics", - "Sequence trimming", - "RNA-Seq quantification", - "Expression analysis", - "Read mapping" - ], - "EDAM topic": [ - "RNA-Seq", - "Transcriptomics", - "Mapping", - "Gene transcripts", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/mlbendall/telescope/", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "telescope_assign", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope", - "Galaxy wrapper version": "1.0.3", - "Conda id": "telescope", - "Conda version": "1.0.3", - "EDAM operation (no superclasses)": [ - "Essential dynamics", - "Sequence trimming", - "RNA-Seq quantification", - "Expression analysis", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "RNA-Seq", - "Transcriptomics", - "Mapping", - "Gene transcripts", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tetoolkit", - "Galaxy tool ids": [ - "tetoolkit_tetranscripts" - ], - "Description": "The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hammelllab.labsites.cshl.edu/software/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tetoolkit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/mhammell-laboratory/TEtranscripts", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit", - "Galaxy wrapper version": "2.2.3", - "Conda id": "tetranscripts", - "Conda version": "2.2.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tetyper", - "Galaxy tool ids": [ - "tetyper" - ], - "Description": "Type a specific transposable element (TE) of interest from paired-end sequencing data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/aesheppard/TETyper", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tetyper", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper", - "Galaxy wrapper version": "1.1", - "Conda id": "tetyper", - "Conda version": "1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tn93", - "Galaxy tool ids": [ - "tn93_readreduce", - "tn93", - "tn93_cluster", - "tn93_filter" - ], - "Description": "Compute distances between sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/veg/tn93/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tn93", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93", - "Galaxy wrapper version": "1.0.6", - "Conda id": "tn93", - "Conda version": "1.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tooldistillator", - "Galaxy tool ids": [ - "tooldistillator", - "tooldistillator_summarize" - ], - "Description": "ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files", - "bio.tool id": "tooldistillator", - "bio.tool ids": [ - "tooldistillator" - ], - "biii": null, - "bio.tool name": "ToolDistillator", - "bio.tool description": "ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.", - "EDAM operation": [ - "Data handling", - "Parsing" - ], - "EDAM topic": [ - "Microbiology", - "Bioinformatics", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://gitlab.com/ifb-elixirfr/abromics/tooldistillator", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "tooldistillator", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator", - "Galaxy wrapper version": "0.8.5.0", - "Conda id": "tooldistillator", - "Conda version": "0.8.5.0", - "EDAM operation (no superclasses)": [ - "Parsing" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Bioinformatics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "tracegroomer", - "Galaxy tool ids": [ - "tracegroomer" - ], - "Description": "TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/cbib/TraceGroomer", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer", - "Galaxy wrapper version": "0.1.3", - "Conda id": "tracegroomer", - "Conda version": "0.1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tracy", - "Galaxy tool ids": [ - "tracy_align", - "tracy_assemble", - "tracy_basecall", - "tracy_decompose" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy", - "Galaxy wrapper version": "0.6.1", - "Conda id": "tracy", - "Conda version": "0.7.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "transdecoder", - "Galaxy tool ids": [ - "transdecoder" - ], - "Description": "TransDecoder finds coding regions within transcripts", - "bio.tool id": "TransDecoder", - "bio.tool ids": [ - "TransDecoder" - ], - "biii": null, - "bio.tool name": "TransDecoder", - "bio.tool description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", - "EDAM operation": [ - "Coding region prediction", - "de Novo sequencing", - "De-novo assembly" - ], - "EDAM topic": [ - "Genomics", - "Gene transcripts", - "RNA-Seq", - "Gene expression", - "Sequence assembly", - "Whole genome sequencing" - ], - "Status": "To update", - "Source": "https://transdecoder.github.io/", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": "transdecoder", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder", - "Galaxy wrapper version": "5.5.0", - "Conda id": "transdecoder", - "Conda version": "5.7.1", - "EDAM operation (no superclasses)": [ - "Coding region prediction", - "de Novo sequencing", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Gene transcripts", - "RNA-Seq", - "Gene expression", - "Sequence assembly", - "Whole genome sequencing" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "transit", - "Galaxy tool ids": [ - "gff_to_prot", - "transit_gumbel", - "transit_hmm", - "transit_resampling", - "transit_tn5gaps" - ], - "Description": "TRANSIT", - "bio.tool id": "transit", - "bio.tool ids": [ - "transit" - ], - "biii": null, - "bio.tool name": "TRANSIT", - "bio.tool description": "A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.", - "EDAM operation": [ - "Transposon prediction" - ], - "EDAM topic": [ - "DNA", - "Sequencing", - "Mobile genetic elements" - ], - "Status": "To update", - "Source": "https://github.com/mad-lab/transit/", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit", - "Galaxy wrapper version": "3.0.2", - "Conda id": "transit", - "Conda version": "3.2.3", - "EDAM operation (no superclasses)": [ - "Transposon prediction" - ], - "EDAM topic (no superclasses)": [ - "DNA", - "Sequencing", - "Mobile genetic elements" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "transtermhp", - "Galaxy tool ids": [ - "transtermhp" - ], - "Description": "Finds rho-independent transcription terminators in bacterial genomes", - "bio.tool id": "transtermhp", - "bio.tool ids": [ - "transtermhp" - ], - "biii": null, - "bio.tool name": "TransTermHP", - "bio.tool description": "TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator", - "EDAM operation": [ - "Transcriptional regulatory element prediction" - ], - "EDAM topic": [ - "Transcription factors and regulatory sites" - ], - "Status": "To update", - "Source": "https://transterm.cbcb.umd.edu", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "transtermhp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp", - "Galaxy wrapper version": null, - "Conda id": "transtermhp", - "Conda version": "2.09", - "EDAM operation (no superclasses)": [ - "Transcriptional regulatory element prediction" - ], - "EDAM topic (no superclasses)": [ - "Transcription factors and regulatory sites" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "trimmomatic", - "Galaxy tool ids": [ - "trimmomatic" - ], - "Description": "A flexible read trimming tool for Illumina NGS data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://www.usadellab.org/cms/?page=trimmomatic", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "trimmomatic", - "Galaxy wrapper owner": "pjbriggs", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic", - "Galaxy wrapper version": "0.39", - "Conda id": "trimmomatic", - "Conda version": "0.39", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "trinity", - "Galaxy tool ids": [ - "trinity_abundance_estimates_to_matrix", - "trinity_align_and_estimate_abundance", - "trinity_analyze_diff_expr", - "trinity_contig_exn50_statistic", - "trinity_define_clusters_by_cutting_tree", - "describe_samples", - "trinity_filter_low_expr_transcripts", - "trinity_gene_to_trans_map", - "trinity_run_de_analysis", - "trinity_samples_qccheck", - "trinity_super_transcripts", - "trinity", - "trinity_stats" - ], - "Description": "Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq", - "bio.tool id": "trinity", - "bio.tool ids": [ - "trinity" - ], - "biii": null, - "bio.tool name": "Trinity", - "bio.tool description": "Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.", - "EDAM operation": [ - "Transcriptome assembly" - ], - "EDAM topic": [ - "Transcriptomics", - "Gene expression", - "Gene transcripts" - ], - "Status": "Up-to-date", - "Source": "https://github.com/trinityrnaseq/trinityrnaseq", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity", - "Galaxy wrapper version": "2.15.1", - "Conda id": "trinity", - "Conda version": "2.15.1", - "EDAM operation (no superclasses)": [ - "Transcriptome assembly" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Gene transcripts" - ], - "Available on UseGalaxy.org": 9, - "Available on UseGalaxy.org.au": 13, - "Available on UseGalaxy.eu": 13, - "Available on UseGalaxy.org.fr": 13 - }, - { - "Galaxy wrapper id": "trinotate", - "Galaxy tool ids": [ - "trinotate" - ], - "Description": "Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.", - "bio.tool id": "trinotate", - "bio.tool ids": [ - "trinotate" - ], - "biii": null, - "bio.tool name": "Trinotate", - "bio.tool description": "Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.", - "EDAM operation": [ - "Gene functional annotation" - ], - "EDAM topic": [ - "Gene expression", - "Transcriptomics" - ], - "Status": "To update", - "Source": "https://trinotate.github.io/", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": "trinotate", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate", - "Galaxy wrapper version": "3.2.2", - "Conda id": "trinotate", - "Conda version": "4.0.2", - "EDAM operation (no superclasses)": [ - "Gene functional annotation" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "trycycler", - "Galaxy tool ids": [ - "trycycler_cluster", - "trycycler_consensus", - "trycycler_partition", - "trycycler_reconcile_msa", - "trycycler_subsample" - ], - "Description": "Trycycler toolkit wrappers", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/rrwick/Trycycler", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "trycycler", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler", - "Galaxy wrapper version": "0.5.5", - "Conda id": "trycycler", - "Conda version": "0.5.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "tsebra", - "Galaxy tool ids": [ - "tsebra" - ], - "Description": "This tool has been developed to combine BRAKER predictions.", - "bio.tool id": "tsebra", - "bio.tool ids": [ - "tsebra" - ], - "biii": null, - "bio.tool name": "TSEBRA", - "bio.tool description": "TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.", - "EDAM operation": [ - "Homology-based gene prediction", - "Alternative splicing prediction" - ], - "EDAM topic": [ - "Gene expression", - "RNA-Seq", - "Gene transcripts", - "Model organisms" - ], - "Status": "To update", - "Source": "https://github.com/Gaius-Augustus/TSEBRA", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra", - "Galaxy wrapper version": "1.1.2.4", - "Conda id": "tsebra", - "Conda version": "1.1.2.5", - "EDAM operation (no superclasses)": [ - "Homology-based gene prediction", - "Alternative splicing prediction" - ], - "EDAM topic (no superclasses)": [ - "Gene expression", - "RNA-Seq", - "Gene transcripts", - "Model organisms" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tsne", - "Galaxy tool ids": [ - "tsne" - ], - "Description": "T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cran.r-project.org/web/packages/Rtsne/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "tsne", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne", - "Galaxy wrapper version": "0.0.2", - "Conda id": "r-rtsne", - "Conda version": "0.13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "tximport", - "Galaxy tool ids": [ - "tximport" - ], - "Description": "Wrapper for the Bioconductor package tximport", - "bio.tool id": "tximport", - "bio.tool ids": [ - "tximport" - ], - "biii": null, - "bio.tool name": "tximport", - "bio.tool description": "An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.", - "EDAM operation": [ - "Pathway or network analysis", - "Formatting", - "RNA-Seq analysis" - ], - "EDAM topic": [ - "Transcriptomics", - "Gene transcripts", - "Workflows" - ], - "Status": "To update", - "Source": "http://bioconductor.org/packages/tximport/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "tximport", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport", - "Galaxy wrapper version": "1.22.0", - "Conda id": "bioconductor-tximport", - "Conda version": "1.30.0", - "EDAM operation (no superclasses)": [ - "Pathway or network analysis", - "Formatting", - "RNA-Seq analysis" - ], - "EDAM topic (no superclasses)": [ - "Transcriptomics", - "Gene transcripts", - "Workflows" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ucsc_blat", - "Galaxy tool ids": [ - "ucsc_blat" - ], - "Description": "Standalone blat sequence search command line tool", - "bio.tool id": "blat", - "bio.tool ids": [ - "blat" - ], - "biii": null, - "bio.tool name": "BLAT", - "bio.tool description": "Fast, accurate spliced alignment of DNA sequences.", - "EDAM operation": [ - "Sequence alignment" - ], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "http://genome.ucsc.edu/goldenPath/help/blatSpec.html", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ucsc_blat", - "Galaxy wrapper owner": "yating-l", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat", - "Galaxy wrapper version": "377", - "Conda id": "ucsc-blat", - "Conda version": "445", - "EDAM operation (no superclasses)": [ - "Sequence alignment" - ], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasplit", - "Galaxy tool ids": [ - "fasplit" - ], - "Description": "faSplit is a tool to split a single FASTA file into several files", - "bio.tool id": "UCSC_Genome_Browser_Utilities", - "bio.tool ids": [ - "UCSC_Genome_Browser_Utilities" - ], - "biii": null, - "bio.tool name": "UCSC Genome Browser Utilities", - "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "ucsc_fasplit", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit", - "Galaxy wrapper version": "377", - "Conda id": "ucsc-fasplit", - "Conda version": "377", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fatovcf", - "Galaxy tool ids": [ - "fatovcf" - ], - "Description": "Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs", - "bio.tool id": "UCSC_Genome_Browser_Utilities", - "bio.tool ids": [ - "UCSC_Genome_Browser_Utilities" - ], - "biii": null, - "bio.tool name": "UCSC Genome Browser Utilities", - "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "ucsc_fatovcf", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf", - "Galaxy wrapper version": "448", - "Conda id": "ucsc-fatovcf", - "Conda version": "448", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "twobittofa", - "Galaxy tool ids": [ - "ucsc-twobittofa" - ], - "Description": "twoBitToFa is a tool to convert all or part of .2bit file to FASTA", - "bio.tool id": "UCSC_Genome_Browser_Utilities", - "bio.tool ids": [ - "UCSC_Genome_Browser_Utilities" - ], - "biii": null, - "bio.tool name": "UCSC Genome Browser Utilities", - "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://genome.ucsc.edu/goldenpath/help/twoBit.html", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "ucsc_twobittofa", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa", - "Galaxy wrapper version": "377", - "Conda id": "ucsc-twobittofa", - "Conda version": "455", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "wigtobigwig", - "Galaxy tool ids": [ - "ucsc_wigtobigwig" - ], - "Description": "converts bedGraph (wig) files into binary bigwig", - "bio.tool id": "UCSC_Genome_Browser_Utilities", - "bio.tool ids": [ - "UCSC_Genome_Browser_Utilities" - ], - "biii": null, - "bio.tool name": "UCSC Genome Browser Utilities", - "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", - "EDAM operation": [], - "EDAM topic": [ - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://genome.ucsc.edu/goldenPath/help/bigWig.html", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "ucsc_wigtobigwig", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig", - "Galaxy wrapper version": "447", - "Conda id": "ucsc-wigtobigwig", - "Conda version": "447", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [ - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "umi_tools", - "Galaxy tool ids": [ - "umi_tools_count", - "umi_tools_dedup", - "umi_tools_extract", - "umi_tools_group", - "umi_tools_whitelist" - ], - "Description": "UMI-tools extract - Extract UMIs from fastq", - "bio.tool id": "umi-tools", - "bio.tool ids": [ - "umi-tools" - ], - "biii": null, - "bio.tool name": "UMI-tools", - "bio.tool description": "Tools for handling Unique Molecular Identifiers in NGS data sets.", - "EDAM operation": [ - "Sequencing quality control" - ], - "EDAM topic": [ - "NGS", - "Sequence sites, features and motifs", - "Quality affairs" - ], - "Status": "To update", - "Source": "https://github.com/CGATOxford/UMI-tools", - "ToolShed categories": [ - "Sequence Analysis", - "Transcriptomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools", - "Galaxy wrapper version": "1.1.2", - "Conda id": "umi_tools", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [ - "Sequencing quality control" - ], - "EDAM topic (no superclasses)": [ - "Sequence sites, features and motifs", - "Quality affairs" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "unicycler", - "Galaxy tool ids": [ - "unicycler" - ], - "Description": "Unicycler is a hybrid assembly pipeline for bacterial genomes.", - "bio.tool id": "unicycler", - "bio.tool ids": [ - "unicycler" - ], - "biii": null, - "bio.tool name": "Unicycler", - "bio.tool description": "A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.", - "EDAM operation": [ - "Genome assembly", - "Aggregation" - ], - "EDAM topic": [ - "Microbiology", - "Genomics", - "Sequencing", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/rrwick/Unicycler", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "unicycler", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler", - "Galaxy wrapper version": "0.5.0", - "Conda id": "unicycler", - "Conda version": "0.5.0", - "EDAM operation (no superclasses)": [ - "Genome assembly", - "Aggregation" - ], - "EDAM topic (no superclasses)": [ - "Microbiology", - "Genomics", - "Sequencing", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "usher", - "Galaxy tool ids": [ - "usher_matutils", - "usher" - ], - "Description": "UShER toolkit wrappers", - "bio.tool id": "usher", - "bio.tool ids": [ - "usher" - ], - "biii": null, - "bio.tool name": "usher", - "bio.tool description": "The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.", - "EDAM operation": [ - "Classification", - "Phylogenetic tree visualisation", - "Phylogenetic inference (from molecular sequences)" - ], - "EDAM topic": [ - "Phylogeny", - "Evolutionary biology", - "Cladistics", - "Genotype and phenotype", - "Phylogenomics" - ], - "Status": "To update", - "Source": "https://github.com/yatisht/usher", - "ToolShed categories": [ - "Phylogenetics" - ], - "ToolShed id": "usher", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher", - "Galaxy wrapper version": "0.2.1", - "Conda id": "usher", - "Conda version": "0.6.3", - "EDAM operation (no superclasses)": [ - "Classification", - "Phylogenetic tree visualisation", - "Phylogenetic inference (from molecular sequences)" - ], - "EDAM topic (no superclasses)": [ - "Cladistics", - "Genotype and phenotype", - "Phylogenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "valet", - "Galaxy tool ids": [ - "valet" - ], - "Description": "A pipeline for detecting mis-assemblies in metagenomic assemblies.", - "bio.tool id": "valet", - "bio.tool ids": [ - "valet" - ], - "biii": null, - "bio.tool name": "VALET", - "bio.tool description": "VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.", - "EDAM operation": [ - "Sequence assembly", - "Sequence assembly visualisation" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://github.com/marbl/VALET", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "valet", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet", - "Galaxy wrapper version": null, - "Conda id": "valet", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [ - "Sequence assembly", - "Sequence assembly visualisation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vapor", - "Galaxy tool ids": [ - "vapor" - ], - "Description": "Classify Influenza samples from raw short read sequence data", - "bio.tool id": "vapor", - "bio.tool ids": [ - "vapor" - ], - "biii": null, - "bio.tool name": "VAPOR", - "bio.tool description": "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.", - "EDAM operation": [ - "Data retrieval", - "De-novo assembly", - "Read mapping" - ], - "EDAM topic": [ - "Whole genome sequencing", - "Mapping", - "Sequence assembly" - ], - "Status": "Up-to-date", - "Source": "https://github.com/connor-lab/vapor", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "vapor", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor", - "Galaxy wrapper version": "1.0.2", - "Conda id": "vapor", - "Conda version": "1.0.2", - "EDAM operation (no superclasses)": [ - "Data retrieval", - "De-novo assembly", - "Read mapping" - ], - "EDAM topic (no superclasses)": [ - "Whole genome sequencing", - "Mapping", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vardict", - "Galaxy tool ids": [ - "vardict_java" - ], - "Description": "VarDict - calls SNVs and indels for tumour-normal pairs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AstraZeneca-NGS/VarDictJava", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vardict_java", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict", - "Galaxy wrapper version": "1.8.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "variant_analyzer", - "Galaxy tool ids": [ - "mut2read", - "mut2sscs", - "read2mut" - ], - "Description": "Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "variant_analyzer", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer", - "Galaxy wrapper version": "2.0.0", - "Conda id": "matplotlib", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "varscan", - "Galaxy tool ids": [ - "varscan_copynumber", - "varscan_mpileup", - "varscan_somatic" - ], - "Description": "VarScan is a variant caller for high-throughput sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://dkoboldt.github.io/varscan/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "varscan", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/iuc/tree/master/tools/varscan", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan", - "Galaxy wrapper version": "2.4.3", - "Conda id": "varscan", - "Conda version": "2.4.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "varvamp", - "Galaxy tool ids": [ - "varvamp" - ], - "Description": "Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses", - "bio.tool id": "varvamp", - "bio.tool ids": [ - "varvamp" - ], - "biii": null, - "bio.tool name": "varVAMP", - "bio.tool description": "variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.", - "EDAM operation": [ - "PCR primer design" - ], - "EDAM topic": [ - "Virology" - ], - "Status": "Up-to-date", - "Source": "https://github.com/jonas-fuchs/varVAMP/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "varvamp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/jonas-fuchs/varVAMP", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp", - "Galaxy wrapper version": "1.2.0", - "Conda id": "varvamp", - "Conda version": "1.2.0", - "EDAM operation (no superclasses)": [ - "PCR primer design" - ], - "EDAM topic (no superclasses)": [ - "Virology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf2maf", - "Galaxy tool ids": [ - "vcf2maf" - ], - "Description": "vcf2maf: Convert VCF into MAF", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "vcf2maf", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf", - "Galaxy wrapper version": "1.6.21", - "Conda id": "vcf2maf", - "Conda version": "1.6.22", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcfanno", - "Galaxy tool ids": [ - "vcfanno" - ], - "Description": "Annotate VCF files", - "bio.tool id": "vcfanno", - "bio.tool ids": [ - "vcfanno" - ], - "biii": null, - "bio.tool name": "vcfanno", - "bio.tool description": "Fast, flexible annotation of genetic variants.", - "EDAM operation": [ - "SNP annotation" - ], - "EDAM topic": [ - "Genetic variation", - "Data submission, annotation and curation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/brentp/vcfanno", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfanno", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/vcfanno/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno", - "Galaxy wrapper version": "0.3.5", - "Conda id": "vcfanno", - "Conda version": "0.3.5", - "EDAM operation (no superclasses)": [ - "SNP annotation" - ], - "EDAM topic (no superclasses)": [ - "Genetic variation", - "Data submission, annotation and curation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vegan", - "Galaxy tool ids": [ - "vegan_diversity", - "vegan_fisher_alpha", - "vegan_rarefaction" - ], - "Description": "an R package fo community ecologist", - "bio.tool id": "vegan", - "bio.tool ids": [ - "vegan" - ], - "biii": null, - "bio.tool name": "vegan", - "bio.tool description": "Ordination methods, diversity analysis and other functions for community and vegetation ecologists", - "EDAM operation": [ - "Standardisation and normalisation", - "Analysis" - ], - "EDAM topic": [ - "Ecology", - "Phylogenetics", - "Environmental science" - ], - "Status": "To update", - "Source": "https://cran.r-project.org/package=vegan", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan", - "Galaxy wrapper version": "2.4-3", - "Conda id": "r-vegan", - "Conda version": "2.3_4", - "EDAM operation (no superclasses)": [ - "Standardisation and normalisation", - "Analysis" - ], - "EDAM topic (no superclasses)": [ - "Ecology", - "Phylogenetics", - "Environmental science" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "velocyto", - "Galaxy tool ids": [ - "velocyto_cli" - ], - "Description": "Velocyto is a library for the analysis of RNA velocity.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://velocyto.org/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "velocyto", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto", - "Galaxy wrapper version": "0.17.17", - "Conda id": "velocyto.py", - "Conda version": "0.17.17", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "velvet", - "Galaxy tool ids": [ - "velvetg", - "velveth" - ], - "Description": "de novo genomic assembler specially designed for short read sequencing technologies", - "bio.tool id": "velvet", - "bio.tool ids": [ - "velvet" - ], - "biii": null, - "bio.tool name": "Velvet", - "bio.tool description": "A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.", - "EDAM operation": [ - "Formatting", - "De-novo assembly" - ], - "EDAM topic": [ - "Sequence assembly" - ], - "Status": "To update", - "Source": "https://www.ebi.ac.uk/~zerbino/velvet/", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "velvet", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet", - "Galaxy wrapper version": null, - "Conda id": "velvet", - "Conda version": "1.2.10", - "EDAM operation (no superclasses)": [ - "Formatting", - "De-novo assembly" - ], - "EDAM topic (no superclasses)": [ - "Sequence assembly" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "velvet_optimiser", - "Galaxy tool ids": [ - "velvetoptimiser" - ], - "Description": "Automatically optimize Velvet assemblies", - "bio.tool id": "velvetoptimiser", - "bio.tool ids": [ - "velvetoptimiser" - ], - "biii": null, - "bio.tool name": "VelvetOptimiser", - "bio.tool description": "This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.", - "EDAM operation": [ - "Optimisation and refinement", - "Sequence assembly" - ], - "EDAM topic": [ - "Genomics", - "Sequence assembly" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "velvetoptimiser", - "Galaxy wrapper owner": "simon-gladman", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser", - "Galaxy wrapper version": "2.2.6+galaxy2", - "Conda id": "velvet", - "Conda version": "1.2.10", - "EDAM operation (no superclasses)": [ - "Optimisation and refinement", - "Sequence assembly" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Sequence assembly" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "verkko", - "Galaxy tool ids": [ - "verkko" - ], - "Description": "Telomere-to-telomere assembly pipeline", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/marbl/verkko", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "verkko", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko", - "Galaxy wrapper version": "1.3.1", - "Conda id": "verkko", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vg", - "Galaxy tool ids": [ - "vg_convert", - "vg_deconstruct", - "vg_view" - ], - "Description": "Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/vgteam/vg", - "ToolShed categories": [ - "Sequence Analysis", - "Variant Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg", - "Galaxy wrapper version": "1.23.0", - "Conda id": "vg", - "Conda version": "1.56.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "virAnnot", - "Galaxy tool ids": [ - "virannot_blast2tsv", - "virannot_otu", - "virAnnot_rps2tsv" - ], - "Description": "virAnnot wrappers", - "bio.tool id": "virannot", - "bio.tool ids": [ - "virannot" - ], - "biii": null, - "bio.tool name": "virAnnot", - "bio.tool description": "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project \"Plant Health Bioinformatics Network\". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.", - "EDAM operation": [ - "Sequence annotation", - "Sequence clustering", - "Sequence cluster visualisation" - ], - "EDAM topic": [ - "Metagenomics", - "Virology", - "Microbial ecology" - ], - "Status": "To update", - "Source": "https://github.com/marieBvr/virAnnot", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "virannot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot", - "Galaxy wrapper version": "1.0.0+galaxy0", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [ - "Sequence annotation", - "Sequence clustering", - "Sequence cluster visualisation" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Virology", - "Microbial ecology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "virheat", - "Galaxy tool ids": [ - "virheat" - ], - "Description": "generates a heatmap of allele frequencies from vcf files", - "bio.tool id": "virheat", - "bio.tool ids": [ - "virheat" - ], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/jonas-fuchs/virHEAT", - "ToolShed categories": [ - "Visualization", - "Variant Analysis" - ], - "ToolShed id": "virheat", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat", - "Galaxy wrapper version": "0.7", - "Conda id": "virheat", - "Conda version": "0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "virhunter", - "Galaxy tool ids": [ - "virhunter" - ], - "Description": "Deep Learning method for novel virus detection in sequencing data", - "bio.tool id": "virhunter", - "bio.tool ids": [ - "virhunter" - ], - "biii": null, - "bio.tool name": "VirHunter", - "bio.tool description": "VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).", - "EDAM operation": [ - "Sequence classification" - ], - "EDAM topic": [ - "Virology" - ], - "Status": "To update", - "Source": "https://github.com/cbib/virhunter", - "ToolShed categories": [ - "Machine Learning" - ], - "ToolShed id": "virhunter", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter", - "Galaxy wrapper version": "1.0.0", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Sequence classification" - ], - "EDAM topic (no superclasses)": [ - "Virology" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "volcanoplot", - "Galaxy tool ids": [ - "volcanoplot" - ], - "Description": "Tool to create a Volcano Plot", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://ggplot2.tidyverse.org/", - "ToolShed categories": [ - "Visualization", - "Transcriptomics", - "Statistics" - ], - "ToolShed id": "volcanoplot", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot", - "Galaxy wrapper version": "0.0.6", - "Conda id": "r-ggplot2", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vsearch", - "Galaxy tool ids": [ - "vsearch_alignment", - "vsearch_chimera_detection", - "vsearch_clustering", - "vsearch_dereplication", - "vsearch_masking", - "vsearch_search", - "vsearch_shuffling", - "vsearch_sorting" - ], - "Description": "VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.", - "bio.tool id": "vsearch", - "bio.tool ids": [ - "vsearch" - ], - "biii": null, - "bio.tool name": "VSEARCH", - "bio.tool description": "High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.", - "EDAM operation": [ - "DNA mapping", - "Chimera detection" - ], - "EDAM topic": [ - "Metagenomics", - "Sequence analysis" - ], - "Status": "To update", - "Source": "https://github.com/torognes/vsearch", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "vsearch", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch", - "Galaxy wrapper version": "2.8.3", - "Conda id": "vsearch", - "Conda version": "2.28.1", - "EDAM operation (no superclasses)": [ - "DNA mapping", - "Chimera detection" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 8, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 8 - }, - { - "Galaxy wrapper id": "vsnp", - "Galaxy tool ids": [ - "vsnp_add_zero_coverage", - "vsnp_build_tables", - "vsnp_determine_ref_from_data", - "vsnp_get_snps", - "vsnp_statistics" - ], - "Description": "The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/USDA-VS/vSNP", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "vsnp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp", - "Galaxy wrapper version": "3.0.6", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "weather_app", - "Galaxy tool ids": [ - "simple_weather" - ], - "Description": "provides simple weather in text format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://wttr.in/", - "ToolShed categories": [ - "Visualization", - "Web Services" - ], - "ToolShed id": "simpleweather", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app", - "Galaxy wrapper version": "0.1.2", - "Conda id": "curl", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "weblogo3", - "Galaxy tool ids": [ - "rgweblogo3" - ], - "Description": "Sequence Logo generator for fasta", - "bio.tool id": "weblogo", - "bio.tool ids": [ - "weblogo" - ], - "biii": null, - "bio.tool name": "WebLogo", - "bio.tool description": "Web-based application designed to make generate sequence logos.", - "EDAM operation": [ - "Sequence cluster visualisation", - "Sequence visualisation", - "Sequence motif recognition" - ], - "EDAM topic": [ - "Nucleic acid sites, features and motifs", - "Sequence analysis" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Graphics" - ], - "ToolShed id": "weblogo3", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3", - "Galaxy wrapper version": "3.5.0", - "Conda id": "weblogo", - "Conda version": "3.7.9", - "EDAM operation (no superclasses)": [ - "Sequence cluster visualisation", - "Sequence visualisation", - "Sequence motif recognition" - ], - "EDAM topic (no superclasses)": [ - "Nucleic acid sites, features and motifs", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "windowmasker", - "Galaxy tool ids": [ - "windowmasker_mkcounts", - "windowmasker_ustat" - ], - "Description": "Identify repetitive regions using WindowMasker", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "windowmasker", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker", - "Galaxy wrapper version": "1.0", - "Conda id": "blast", - "Conda version": "2.15.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "winnowmap", - "Galaxy tool ids": [ - "winnowmap" - ], - "Description": "A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/marbl/Winnowmap", - "ToolShed categories": [ - "Next Gen Mappers" - ], - "ToolShed id": "winnowmap", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap", - "Galaxy wrapper version": "2.03", - "Conda id": "winnowmap", - "Conda version": "2.03", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "xpath", - "Galaxy tool ids": [ - "xpath" - ], - "Description": "XPath XML querying tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://search.cpan.org/dist/XML-XPath/", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "xpath", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath", - "Galaxy wrapper version": null, - "Conda id": "perl-xml-xpath", - "Conda version": "1.47", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "yahs", - "Galaxy tool ids": [ - "yahs" - ], - "Description": "Yet Another Hi-C scaffolding tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/c-zhou/yahs", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "yahs", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs", - "Galaxy wrapper version": "1.2a.2", - "Conda id": "yahs", - "Conda version": "1.2a.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "zerone", - "Galaxy tool ids": [ - "zerone" - ], - "Description": "ChIP-seq discretization and quality control", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/nanakiksc/zerone", - "ToolShed categories": [ - "ChIP-seq" - ], - "ToolShed id": "zerone", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone", - "Galaxy wrapper version": "1.0", - "Conda id": "zerone", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bamtools", - "Galaxy tool ids": [ - "bamtools" - ], - "Description": "Operate on and transform BAM datasets in various ways using bamtools", - "bio.tool id": "bamtools", - "bio.tool ids": [ - "bamtools" - ], - "biii": null, - "bio.tool name": "BamTools", - "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", - "EDAM operation": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic": [ - "Sequencing", - "Data management", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pezmaster31/bamtools", - "ToolShed categories": [ - "Sequence Analysis", - "SAM" - ], - "ToolShed id": "bamtools", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools", - "Galaxy wrapper version": "2.5.2", - "Conda id": "bamtools", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bamtools_filter", - "Galaxy tool ids": [ - "bamFilter" - ], - "Description": "Filter BAM datasets on various attributes using bamtools filter", - "bio.tool id": "bamtools", - "bio.tool ids": [ - "bamtools" - ], - "biii": null, - "bio.tool name": "BamTools", - "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", - "EDAM operation": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic": [ - "Sequencing", - "Data management", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pezmaster31/bamtools", - "ToolShed categories": [ - "Sequence Analysis", - "SAM" - ], - "ToolShed id": "bamtools_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter", - "Galaxy wrapper version": "2.5.2", - "Conda id": "bamtools", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "bamtools_split", - "Galaxy tool ids": [ - "bamtools_split_mapped", - "bamtools_split_paired", - "bamtools_split_ref", - "bamtools_split_tag" - ], - "Description": "Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.", - "bio.tool id": "bamtools", - "bio.tool ids": [ - "bamtools" - ], - "biii": null, - "bio.tool name": "BamTools", - "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", - "EDAM operation": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic": [ - "Sequencing", - "Data management", - "Sequence analysis" - ], - "Status": "Up-to-date", - "Source": "https://github.com/pezmaster31/bamtools", - "ToolShed categories": [ - "Sequence Analysis", - "SAM" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split", - "Galaxy wrapper version": "2.5.2", - "Conda id": "bamtools", - "Conda version": "2.5.2", - "EDAM operation (no superclasses)": [ - "Data handling", - "Sequence alignment analysis" - ], - "EDAM topic (no superclasses)": [ - "Sequencing", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biotradis", - "Galaxy tool ids": [ - "bacteria_tradis", - "tradis_essentiality", - "tradis_gene_insert_sites" - ], - "Description": "Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.", - "bio.tool id": "biotradis", - "bio.tool ids": [ - "biotradis" - ], - "biii": null, - "bio.tool name": "biotradis", - "bio.tool description": "The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.", - "EDAM operation": [ - "Sequence analysis" - ], - "EDAM topic": [ - "Mobile genetic elements", - "Workflows" - ], - "Status": "Up-to-date", - "Source": "https://www.sanger.ac.uk/science/tools/bio-tradis", - "ToolShed categories": [ - "Genome annotation" - ], - "ToolShed id": "biotradis", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis", - "Galaxy wrapper version": "1.4.5", - "Conda id": "biotradis", - "Conda version": "1.4.5", - "EDAM operation (no superclasses)": [ - "Sequence analysis" - ], - "EDAM topic (no superclasses)": [ - "Mobile genetic elements", - "Workflows" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cuffcompare", - "Galaxy tool ids": [ - "cuffcompare" - ], - "Description": "Galaxy wrappers for the Cuffcompare tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cuffcompare", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cuffdiff", - "Galaxy tool ids": [ - "cuffdiff" - ], - "Description": "Galaxy wrappers for the Cuffdiff tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cuffdiff", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cufflinks", - "Galaxy tool ids": [ - "cufflinks" - ], - "Description": "Galaxy wrappers for the Cufflinks tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cufflinks", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cuffmerge", - "Galaxy tool ids": [ - "cuffmerge" - ], - "Description": "Galaxy wrappers for the Cuffmerge tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cuffmerge", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "cuffnorm", - "Galaxy tool ids": [ - "cuffnorm" - ], - "Description": "The Cuffnorm tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cuffnorm", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cuffquant", - "Galaxy tool ids": [ - "cuffquant" - ], - "Description": "The Cuffquant tool", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://cole-trapnell-lab.github.io/cufflinks/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cuffquant", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant", - "Galaxy wrapper version": "2.2.1", - "Conda id": "cufflinks", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_clipping_histogram", - "Galaxy tool ids": [ - "cshl_fasta_clipping_histogram" - ], - "Description": "Length Distribution chart", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Graphics", - "Statistics" - ], - "ToolShed id": "fasta_clipping_histogram", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_formatter", - "Galaxy tool ids": [ - "cshl_fasta_formatter" - ], - "Description": "FASTA Width formatter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_formatter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fasta_nucleotide_changer", - "Galaxy tool ids": [ - "cshl_fasta_nucleotides_changer" - ], - "Description": "RNA/DNA converter.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_nucleotide_changer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_quality_boxplot", - "Galaxy tool ids": [ - "cshl_fastq_quality_boxplot" - ], - "Description": "Draw quality score boxplot", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation", - "Graphics", - "Statistics" - ], - "ToolShed id": "fastq_quality_boxplot", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_quality_converter", - "Galaxy tool ids": [ - "cshl_fastq_quality_converter" - ], - "Description": "Quality format converter (ASCII-Numeric)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_quality_converter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_quality_filter", - "Galaxy tool ids": [ - "cshl_fastq_quality_filter" - ], - "Description": "Filter by quality", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_quality_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_to_fasta", - "Galaxy tool ids": [ - "cshl_fastq_to_fasta" - ], - "Description": "FASTQ to FASTA converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Convert Formats" - ], - "ToolShed id": "fastq_to_fasta", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_artifacts_filter", - "Galaxy tool ids": [ - "cshl_fastx_artifacts_filter" - ], - "Description": "Remove sequencing artifacts", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "fastx_artifacts_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_barcode_splitter", - "Galaxy tool ids": [ - "cshl_fastx_barcode_splitter" - ], - "Description": "Barcode Splitter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "fastx_barcode_splitter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_clipper", - "Galaxy tool ids": [ - "cshl_fastx_clipper" - ], - "Description": "Clip adapter sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "fastx_clipper", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_collapser", - "Galaxy tool ids": [ - "cshl_fastx_collapser" - ], - "Description": "Collapse sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fastx_collapser", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_nucleotides_distribution", - "Galaxy tool ids": [ - "cshl_fastx_nucleotides_distribution" - ], - "Description": "Draw nucleotides distribution chart", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation", - "Graphics" - ], - "ToolShed id": "fastx_nucleotides_distribution", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_quality_statistics", - "Galaxy tool ids": [ - "cshl_fastx_quality_statistics" - ], - "Description": "Compute quality statistics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation", - "Statistics" - ], - "ToolShed id": "fastx_quality_statistics", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_renamer", - "Galaxy tool ids": [ - "cshl_fastx_renamer" - ], - "Description": "Rename sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "fastx_renamer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_reverse_complement", - "Galaxy tool ids": [ - "cshl_fastx_reverse_complement" - ], - "Description": "Reverse-Complement", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fastq Manipulation", - "Fasta Manipulation" - ], - "ToolShed id": "fastx_reverse_complement", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastx_trimmer", - "Galaxy tool ids": [ - "cshl_fastx_trimmer" - ], - "Description": "Trim sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", - "ToolShed categories": [ - "Fasta Manipulation", - "Fastq Manipulation" - ], - "ToolShed id": "fastx_trimmer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer", - "Galaxy wrapper version": "0.0.14", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_combiner", - "Galaxy tool ids": [ - "fastq_combiner" - ], - "Description": "Combine FASTA and QUAL into FASTQ", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation", - "Fasta Manipulation" - ], - "ToolShed id": "fastq_combiner", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_filter", - "Galaxy tool ids": [ - "fastq_filter" - ], - "Description": "Filter FASTQ reads by quality score and length", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_filter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_groomer", - "Galaxy tool ids": [ - "fastq_groomer" - ], - "Description": "Convert between various FASTQ quality formats.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_groomer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_manipulation", - "Galaxy tool ids": [ - "fastq_manipulation" - ], - "Description": "Manipulate FASTQ reads on various attributes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_manipulation", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_masker_by_quality", - "Galaxy tool ids": [ - "fastq_masker_by_quality" - ], - "Description": "FASTQ Masker by quality score", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_masker_by_quality", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_paired_end_deinterlacer", - "Galaxy tool ids": [ - "fastq_paired_end_deinterlacer" - ], - "Description": "FASTQ de-interlacer on paired end reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_paired_end_deinterlacer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_paired_end_interlacer", - "Galaxy tool ids": [ - "fastq_paired_end_interlacer" - ], - "Description": "FASTQ interlacer on paired end reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_paired_end_interlacer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_paired_end_joiner", - "Galaxy tool ids": [ - "fastq_paired_end_joiner" - ], - "Description": "FASTQ joiner on paired end reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_paired_end_joiner", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_paired_end_splitter", - "Galaxy tool ids": [ - "fastq_paired_end_splitter" - ], - "Description": "FASTQ splitter on joined paired end reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_paired_end_splitter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_stats", - "Galaxy tool ids": [ - "fastq_stats" - ], - "Description": "FASTQ Summary Statistics by column", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_stats", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_to_tabular", - "Galaxy tool ids": [ - "fastq_to_tabular" - ], - "Description": "FASTQ to Tabular converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_to_tabular", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastq_trimmer", - "Galaxy tool ids": [ - "fastq_trimmer" - ], - "Description": "FASTQ Trimmer by quality", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_trimmer", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastqtofasta", - "Galaxy tool ids": [ - "fastq_to_fasta_python" - ], - "Description": "FASTQ to FASTA converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastqtofasta", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tabular_to_fastq", - "Galaxy tool ids": [ - "tabular_to_fastq" - ], - "Description": "Tabular to FASTQ converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproject/sequence_utils", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "tabular_to_fastq", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq", - "Galaxy wrapper version": "1.1.5", - "Conda id": "galaxy_sequence_utils", - "Conda version": "1.1.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "kraken", - "Galaxy tool ids": [ - "kraken-filter", - "kraken-mpa-report", - "kraken-report", - "kraken-translate", - "kraken" - ], - "Description": "Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.", - "bio.tool id": "kraken", - "bio.tool ids": [ - "kraken" - ], - "biii": null, - "bio.tool name": "Kraken", - "bio.tool description": "System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.", - "EDAM operation": [ - "Taxonomic classification" - ], - "EDAM topic": [ - "Taxonomy", - "Metagenomics" - ], - "Status": "To update", - "Source": "http://ccb.jhu.edu/software/kraken/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kraken", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken", - "Galaxy wrapper version": null, - "Conda id": "kraken", - "Conda version": "1.1.1", - "EDAM operation (no superclasses)": [ - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy", - "Metagenomics" - ], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "kraken2", - "Galaxy tool ids": [ - "kraken2" - ], - "Description": "Kraken2 for taxonomic designation.", - "bio.tool id": "kraken2", - "bio.tool ids": [ - "kraken2" - ], - "biii": null, - "bio.tool name": "kraken2", - "bio.tool description": "Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.", - "EDAM operation": [ - "Taxonomic classification" - ], - "EDAM topic": [ - "Taxonomy", - "Metagenomics" - ], - "Status": "To update", - "Source": "http://ccb.jhu.edu/software/kraken/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "kraken2", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2", - "Galaxy wrapper version": "2.1.1", - "Conda id": "kraken2", - "Conda version": "2.1.3", - "EDAM operation (no superclasses)": [ - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Taxonomy", - "Metagenomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "samtools", - "Galaxy tool ids": [], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/samtools/samtools", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools", - "Galaxy wrapper version": "1.15.1", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snpeff", - "Galaxy tool ids": [ - "snpEff", - "snpEff_build_gb", - "snpEff_databases", - "snpEff_download", - "snpEff_get_chr_names" - ], - "Description": "SnpEff is a genetic variant annotation and effect prediction toolbox", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://snpeff.sourceforge.net/", - "ToolShed categories": [ - "Genome-Wide Association Study", - "Variant Analysis" - ], - "ToolShed id": "snpeff", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff", - "Galaxy wrapper version": null, - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "snpsift", - "Galaxy tool ids": [ - "snpSift_annotate", - "snpSift_caseControl", - "snpSift_extractFields", - "snpSift_filter", - "snpSift_int", - "snpSift_rmInfo", - "snpsift_vartype", - "snpSift_vcfCheck" - ], - "Description": "snpEff SnpSift tools from Pablo Cingolani", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://snpeff.sourceforge.net/SnpSift.html", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snpsift", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift", - "Galaxy wrapper version": null, - "Conda id": "snpsift", - "Conda version": "5.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 8, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 8 - }, - { - "Galaxy wrapper id": "snpsift_dbnsfp", - "Galaxy tool ids": [ - "snpSift_dbnsfp" - ], - "Description": "snpEff SnpSift dbnsfp tool from Pablo Cingolani", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://snpeff.sourceforge.net/SnpSift.html#dbNSFP", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snpsift_dbnsfp", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp", - "Galaxy wrapper version": null, - "Conda id": "snpsift", - "Conda version": "5.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snpsift_genesets", - "Galaxy tool ids": [ - "snpSift_geneSets" - ], - "Description": "Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://snpeff.sourceforge.net/SnpSift.html#geneSets", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snpsift_genesets", - "Galaxy wrapper owner": "iuc", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets", - "Galaxy wrapper version": null, - "Conda id": "snpsift", - "Conda version": "5.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf2tsv", - "Galaxy tool ids": [ - "vcf2tsv" - ], - "Description": "Converts VCF files into tab-delimited format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis", - "Convert Formats" - ], - "ToolShed id": "vcf2tsv", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfaddinfo", - "Galaxy tool ids": [ - "vcfaddinfo" - ], - "Description": "Adds info fields from the second dataset which are not present in the first dataset.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfaddinfo", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfallelicprimitives", - "Galaxy tool ids": [ - "vcfallelicprimitives" - ], - "Description": "Splits alleleic primitives (gaps or mismatches) into multiple VCF lines", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfallelicprimitives", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfannotate", - "Galaxy tool ids": [ - "vcfannotate" - ], - "Description": "Intersect VCF records with BED annotations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfannotate", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfannotategenotypes", - "Galaxy tool ids": [ - "vcfannotategenotypes" - ], - "Description": "Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfannotategenotypes", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfbedintersect", - "Galaxy tool ids": [ - "vcfbedintersect" - ], - "Description": "Intersect VCF and BED datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfbedintersect", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfbreakcreatemulti", - "Galaxy tool ids": [ - "vcfbreakcreatemulti" - ], - "Description": "Break multiple alleles into multiple records, or combine overallpoing alleles into a single record", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfbreakcreatemulti", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfcheck", - "Galaxy tool ids": [ - "vcfcheck" - ], - "Description": "Verify that the reference allele matches the reference genome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfcheck", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfcombine", - "Galaxy tool ids": [ - "vcfcombine" - ], - "Description": "Combine multiple VCF datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfcombine", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfcommonsamples", - "Galaxy tool ids": [ - "vcfcommonsamples" - ], - "Description": "Output records belonging to samples commong between two datasets.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfcommonsamples", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfdistance", - "Galaxy tool ids": [ - "vcfdistance" - ], - "Description": "Calculate distance to the nearest variant.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfdistance", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcffilter", - "Galaxy tool ids": [ - "vcffilter2" - ], - "Description": "Tool for filtering VCF files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcffilter", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcffixup", - "Galaxy tool ids": [ - "vcffixup" - ], - "Description": "Count the allele frequencies across alleles present in each record in the VCF file.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcffixup", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfflatten", - "Galaxy tool ids": [ - "vcfflatten2" - ], - "Description": "Removes multi-allelic sites by picking the most common alternate", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfflatten", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfgeno2haplo", - "Galaxy tool ids": [ - "vcfgeno2haplo" - ], - "Description": "Convert genotype-based phased alleles into haplotype alleles", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfgeno2haplo", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfgenotypes", - "Galaxy tool ids": [ - "vcfgenotypes" - ], - "Description": "Convert numerical representation of genotypes to allelic.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfgenotypes", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfhethom", - "Galaxy tool ids": [ - "vcfhethom" - ], - "Description": "Count the number of heterozygotes and alleles, compute het/hom ratio.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfhethom", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfleftalign", - "Galaxy tool ids": [ - "vcfleftalign" - ], - "Description": "Left-align indels and complex variants in VCF dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfleftalign", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfprimers", - "Galaxy tool ids": [ - "vcfprimers" - ], - "Description": "Extract flanking sequences for each VCF record", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfprimers", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfrandomsample", - "Galaxy tool ids": [ - "vcfrandomsample" - ], - "Description": "Randomly sample sites from VCF dataset", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfrandomsample", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfselectsamples", - "Galaxy tool ids": [ - "vcfselectsamples" - ], - "Description": "Select samples from a VCF file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfselectsamples", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfsort", - "Galaxy tool ids": [ - "vcfsort" - ], - "Description": "Sort VCF dataset by coordinate", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfsort", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "vcfvcfintersect", - "Galaxy tool ids": [ - "vcfvcfintersect" - ], - "Description": "Intersect two VCF datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ekg/vcflib", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "vcfvcfintersect", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect", - "Galaxy wrapper version": null, - "Conda id": "vcflib", - "Conda version": "1.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - } - ], - [ - { - "Galaxy wrapper id": "ThermoRawFileParser", - "Galaxy tool ids": [ - "thermo_raw_file_converter" - ], - "Description": "Thermo RAW file converter", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/compomics/ThermoRawFileParser", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "thermo_raw_file_converter", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser", - "Galaxy wrapper version": "1.3.4", - "Conda id": "thermorawfileparser", - "Conda version": "1.4.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "appendfdr", - "Galaxy tool ids": [ - "append_fdr" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "appendfdr", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr", - "Galaxy wrapper version": "0.2.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bed_to_protein_map", - "Galaxy tool ids": [ - "bed_to_protein_map" - ], - "Description": "Converts a BED file to a tabular list of exon locations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "bed_to_protein_map", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map", - "Galaxy wrapper version": "0.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast_plus_remote_blastp", - "Galaxy tool ids": [ - "blast_plus_remote_blastp" - ], - "Description": "NCBI BLAST+ with -remote option", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://blast.ncbi.nlm.nih.gov/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "blast_plus_remote_blastp", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp", - "Galaxy wrapper version": "2.6.0", - "Conda id": "blast", - "Conda version": "2.15.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bumbershoot", - "Galaxy tool ids": [ - "idpqonvertEmbedder", - "idpassemble", - "idpqonvert", - "idpquery", - "myrimatch" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://proteowizard.sourceforge.net/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot", - "Galaxy wrapper version": "3.0.21142", - "Conda id": "bumbershoot", - "Conda version": "3_0_21142_0e4f4a4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "calisp", - "Galaxy tool ids": [ - "calisp" - ], - "Description": "Calgary approach to isotopes in proteomics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/kinestetika/Calisp/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "calisp", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp", - "Galaxy wrapper version": "3.0.13", - "Conda id": "calisp", - "Conda version": "3.0.13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cardinal", - "Galaxy tool ids": [ - "cardinal_classification", - "cardinal_colocalization", - "cardinal_combine", - "cardinal_data_exporter", - "cardinal_filtering", - "cardinal_mz_images", - "cardinal_preprocessing", - "cardinal_quality_report", - "cardinal_segmentations", - "cardinal_single_ion_segmentation", - "cardinal_spectra_plots" - ], - "Description": "Statistical and computational tools for analyzing mass spectrometry imaging datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://cardinalmsi.org", - "ToolShed categories": [ - "Proteomics", - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal", - "Galaxy wrapper version": "2.10.0", - "Conda id": "bioconductor-cardinal", - "Conda version": "3.4.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 9, - "Available on UseGalaxy.eu": 11, - "Available on UseGalaxy.org.fr": 11 - }, - { - "Galaxy wrapper id": "dbbuilder", - "Galaxy tool ids": [ - "dbbuilder" - ], - "Description": "Protein Database Downloader", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "dbbuilder", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", - "Galaxy wrapper version": "0.3.4", - "Conda id": "wget", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "decoyfasta", - "Galaxy tool ids": [], - "Description": "Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "decoyfasta", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dia_umpire", - "Galaxy tool ids": [ - "dia_umpire_se" - ], - "Description": "DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://diaumpire.sourceforge.net/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "dia_umpire", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire", - "Galaxy wrapper version": "2.1.3", - "Conda id": "dia_umpire", - "Conda version": "2.1.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dialignr", - "Galaxy tool ids": [ - "dialignr" - ], - "Description": "DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/shubham1637/DIAlignR", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "dialignr", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr", - "Galaxy wrapper version": "1.2.0", - "Conda id": "bioconductor-dialignr", - "Conda version": "2.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "diann", - "Galaxy tool ids": [ - "diann" - ], - "Description": "DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/vdemichev/DiaNN", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "diann", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/vdemichev/DiaNN", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann", - "Galaxy wrapper version": "1.8.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "diapysef", - "Galaxy tool ids": [ - "diapysef" - ], - "Description": "diapysef is a convenience package for working with DIA-PASEF data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pypi.org/project/diapysef/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "diapysef", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef", - "Galaxy wrapper version": "0.3.5.0", - "Conda id": "diapysef", - "Conda version": "1.0.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "diffacto", - "Galaxy tool ids": [ - "diffacto" - ], - "Description": "Diffacto comparative protein abundance estimation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/statisticalbiotechnology/diffacto", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "diffacto", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto", - "Galaxy wrapper version": "1.0.6", - "Conda id": "diffacto", - "Conda version": "1.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "digestdb", - "Galaxy tool ids": [ - "digestdb" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "digestdb", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb", - "Galaxy wrapper version": "0.1.0", - "Conda id": "trans_proteomic_pipeline", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "directag_and_tagrecon", - "Galaxy tool ids": [], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "directag_and_tagrecon", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "data_manager_eggnog_mapper", - "Galaxy tool ids": [], - "Description": "downloads eggnog data for eggnog-mapper", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "data_manager_eggnog_mapper", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "data_manager_eggnog_mapper_abspath", - "Galaxy tool ids": [], - "Description": "download eggnog data for eggnog-mapper", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "data_manager_eggnog_mapper_abspath", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "eggnog_mapper", - "Galaxy tool ids": [ - "eggnog_mapper", - "eggnog_mapper_annotate", - "eggnog_mapper_search" - ], - "Description": "eggnog-mapper fast functional annotation of novel sequences", - "bio.tool id": "eggnog-mapper-v2", - "bio.tool ids": [ - "eggnog-mapper-v2" - ], - "biii": null, - "bio.tool name": "eggNOG-mapper v2", - "bio.tool description": "EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.", - "EDAM operation": [ - "Homology-based gene prediction", - "Genome annotation", - "Fold recognition", - "Information extraction", - "Query and retrieval" - ], - "EDAM topic": [ - "Metagenomics", - "Phylogeny", - "Transcriptomics", - "Workflows", - "Sequence analysis" - ], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "eggnog_mapper", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper", - "Galaxy wrapper version": "2.1.8", - "Conda id": "eggnog-mapper", - "Conda version": "2.1.12", - "EDAM operation (no superclasses)": [ - "Homology-based gene prediction", - "Genome annotation", - "Fold recognition", - "Information extraction", - "Query and retrieval" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Phylogeny", - "Transcriptomics", - "Workflows", - "Sequence analysis" - ], - "Available on UseGalaxy.org": 3, - "Available on UseGalaxy.org.au": 3, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "encyclopedia", - "Galaxy tool ids": [ - "encyclopedia_encyclopedia", - "encyclopedia_fasta_to_prosit_csv", - "encyclopedia_library_to_blib", - "encyclopedia_prosit_csv_to_library", - "encyclopedia_quantify", - "encyclopedia_searchtolib", - "encyclopedia_walnut" - ], - "Description": "Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bitbucket.org/searleb/encyclopedia/wiki/Home", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "encyclopedia", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia", - "Galaxy wrapper version": "1.12.34", - "Conda id": "encyclopedia", - "Conda version": "2.12.30", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fasta_merge_files_and_filter_unique_sequences", - "Galaxy tool ids": [ - "fasta_merge_files_and_filter_unique_sequences" - ], - "Description": "Concatenate FASTA database files together", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/tools-galaxyp/", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "fasta_merge_files_and_filter_unique_sequences", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences", - "Galaxy wrapper version": "1.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "fastg2protlib", - "Galaxy tool ids": [ - "fastg2protlib-peptides", - "fastg2protlib-validate" - ], - "Description": "Generate FASTA from FASTG", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/fastg2protlib.git", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "fastg2protlib", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib", - "Galaxy wrapper version": "1.0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "feature_alignment", - "Galaxy tool ids": [ - "feature_alignment" - ], - "Description": "TRIC integrates information from all available runs via a graph-based alignment strategy", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "feature_alignment", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment", - "Galaxy wrapper version": "0.11.0", - "Conda id": "msproteomicstools", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_by_fasta_ids", - "Galaxy tool ids": [ - "filter_by_fasta_ids" - ], - "Description": "Filter FASTA on the headers and/or the sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation", - "Proteomics" - ], - "ToolShed id": "filter_by_fasta_ids", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids", - "Galaxy wrapper version": "2.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "flashlfq", - "Galaxy tool ids": [ - "flashlfq" - ], - "Description": "FlashLFQ mass-spectrometry proteomics label-free quantification", - "bio.tool id": "flashlfq", - "bio.tool ids": [ - "flashlfq" - ], - "biii": null, - "bio.tool name": "FlashLFQ", - "bio.tool description": "FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.", - "EDAM operation": [ - "Label-free quantification" - ], - "EDAM topic": [ - "Proteomics experiment", - "Proteomics" - ], - "Status": "To update", - "Source": "https://github.com/smith-chem-wisc/FlashLFQ", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "flashlfq", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq", - "Galaxy wrapper version": "1.0.3.1", - "Conda id": "flashlfq", - "Conda version": "1.2.6", - "EDAM operation (no superclasses)": [ - "Label-free quantification" - ], - "EDAM topic (no superclasses)": [ - "Proteomics experiment", - "Proteomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gffcompare_to_bed", - "Galaxy tool ids": [ - "gffcompare_to_bed" - ], - "Description": "Filter and convert a gffCompare GTF to BED", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/gpertea/gffcompare/", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "gffcompare_to_bed", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed", - "Galaxy wrapper version": "0.2.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hardklor", - "Galaxy tool ids": [ - "hardklor", - "kronik" - ], - "Description": "Hardklör", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "hardklor", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor", - "Galaxy wrapper version": "2.30.1+galaxy1", - "Conda id": "hardklor", - "Conda version": "2.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "idconvert", - "Galaxy tool ids": [ - "idconvert" - ], - "Description": "Convert mass spectrometry identification files on linux or MacOSX", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "idconvert", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert", - "Galaxy wrapper version": null, - "Conda id": "proteowizard", - "Conda version": "3_0_9992", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lfq_protein_quant", - "Galaxy tool ids": [ - "lfq_protein_quant" - ], - "Description": "Enable protein summarisation and quantitation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/compomics/LFQ_galaxy_p", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "lfq_protein_quant", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant", - "Galaxy wrapper version": "1.0", - "Conda id": "bioconductor-msnbase", - "Conda version": "2.28.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ltq_iquant_cli", - "Galaxy tool ids": [], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "ltq_iquant_cli", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "maldiquant", - "Galaxy tool ids": [ - "maldi_quant_peak_detection", - "maldi_quant_preprocessing" - ], - "Description": "MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://strimmerlab.org/software/maldiquant/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "MALDIquant", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant", - "Galaxy wrapper version": "1.22.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "map_peptides_to_bed", - "Galaxy tool ids": [ - "map_peptides_to_bed" - ], - "Description": "Map peptides to a reference genome for display by a genome browser", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "map_peptides_to_bed", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed", - "Galaxy wrapper version": "0.2", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "maxquant", - "Galaxy tool ids": [ - "maxquant", - "maxquant_mqpar" - ], - "Description": "wrapper for MaxQuant", - "bio.tool id": "maxquant", - "bio.tool ids": [ - "maxquant" - ], - "biii": null, - "bio.tool name": "MaxQuant", - "bio.tool description": "Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.", - "EDAM operation": [ - "Imputation", - "Visualisation", - "Protein quantification", - "Statistical calculation", - "Standardisation and normalisation", - "Heat map generation", - "Clustering", - "Principal component plotting" - ], - "EDAM topic": [ - "Proteomics experiment", - "Proteomics", - "Statistics and probability" - ], - "Status": "Up-to-date", - "Source": "https://www.maxquant.org/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "maxquant", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant", - "Galaxy wrapper version": "2.0.3.0", - "Conda id": "maxquant", - "Conda version": "2.0.3.0", - "EDAM operation (no superclasses)": [ - "Imputation", - "Visualisation", - "Protein quantification", - "Standardisation and normalisation", - "Heat map generation", - "Clustering" - ], - "EDAM topic (no superclasses)": [ - "Proteomics experiment", - "Proteomics", - "Statistics and probability" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "meta_proteome_analyzer", - "Galaxy tool ids": [ - "meta_proteome_analyzer" - ], - "Description": "MetaProteomeAnalyzer", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/compomics/meta-proteome-analyzer/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "meta_proteome_analyzer", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer", - "Galaxy wrapper version": "2.0.0", - "Conda id": "mpa-portable", - "Conda version": "2.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metagene_annotator", - "Galaxy tool ids": [ - "metagene_annotator" - ], - "Description": "MetaGeneAnnotator gene-finding program for prokaryote and phage", - "bio.tool id": "metageneannotator", - "bio.tool ids": [ - "metageneannotator" - ], - "biii": null, - "bio.tool name": "MetaGeneAnnotator", - "bio.tool description": "Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.", - "EDAM operation": [ - "Sequence annotation" - ], - "EDAM topic": [ - "Genomics", - "Model organisms", - "Data submission, annotation and curation" - ], - "Status": "Up-to-date", - "Source": "http://metagene.nig.ac.jp/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "metagene_annotator", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator", - "Galaxy wrapper version": "1.0", - "Conda id": "metagene_annotator", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [ - "Sequence annotation" - ], - "EDAM topic (no superclasses)": [ - "Genomics", - "Model organisms", - "Data submission, annotation and curation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metanovo", - "Galaxy tool ids": [ - "metanovo" - ], - "Description": "Produce targeted databases for mass spectrometry analysis.", - "bio.tool id": "metanovo", - "bio.tool ids": [ - "metanovo" - ], - "biii": null, - "bio.tool name": "MetaNovo", - "bio.tool description": "An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.", - "EDAM operation": [ - "Target-Decoy", - "de Novo sequencing", - "Tag-based peptide identification", - "Protein identification", - "Expression analysis" - ], - "EDAM topic": [ - "Proteomics", - "Microbial ecology", - "Metagenomics", - "Proteomics experiment", - "Small molecules" - ], - "Status": "Up-to-date", - "Source": "https://github.com/uct-cbio/proteomics-pipelines", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "metanovo", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo", - "Galaxy wrapper version": "1.9.4", - "Conda id": "metanovo", - "Conda version": "1.9.4", - "EDAM operation (no superclasses)": [ - "Target-Decoy", - "de Novo sequencing", - "Tag-based peptide identification", - "Protein identification", - "Expression analysis" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Microbial ecology", - "Metagenomics", - "Proteomics experiment", - "Small molecules" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "metaquantome", - "Galaxy tool ids": [ - "metaquantome_db", - "metaquantome_expand", - "metaquantome_filter", - "metaquantome_sample", - "metaquantome_stat", - "metaquantome_viz" - ], - "Description": "quantitative analysis of microbiome taxonomy and function", - "bio.tool id": "metaQuantome", - "bio.tool ids": [ - "metaQuantome" - ], - "biii": null, - "bio.tool name": "metaQuantome", - "bio.tool description": "metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.", - "EDAM operation": [ - "Principal component visualisation", - "Visualisation", - "Functional clustering", - "Query and retrieval", - "Differential protein expression analysis", - "Heat map generation", - "Quantification", - "Indexing", - "Filtering", - "Statistical inference" - ], - "EDAM topic": [ - "Proteomics", - "Metatranscriptomics", - "Microbial ecology", - "Proteomics experiment", - "Metagenomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/galaxyproteomics/metaquantome/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "metaquantome", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome", - "Galaxy wrapper version": "2.0.2", - "Conda id": "metaquantome", - "Conda version": "2.0.2", - "EDAM operation (no superclasses)": [ - "Principal component visualisation", - "Functional clustering", - "Query and retrieval", - "Heat map generation", - "Quantification", - "Indexing", - "Filtering", - "Statistical inference" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Metatranscriptomics", - "Microbial ecology", - "Proteomics experiment", - "Metagenomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 6, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mgf_formatter", - "Galaxy tool ids": [ - "mgf_formatter" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "mgf_formatter", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter", - "Galaxy wrapper version": "1.0.0", - "Conda id": "mgf-formatter", - "Conda version": "1.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "moFF", - "Galaxy tool ids": [ - "proteomics_moff" - ], - "Description": "moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/compomics/moFF", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomics_moff", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF", - "Galaxy wrapper version": "2.0.3", - "Conda id": "moff", - "Conda version": "2.0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "morpheus", - "Galaxy tool ids": [ - "morpheus" - ], - "Description": "Morpheus MS Search Application", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "morpheus", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus", - "Galaxy wrapper version": "2.255.0", - "Conda id": "morpheus", - "Conda version": "288", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mqppep", - "Galaxy tool ids": [ - "mqppep_anova", - "mqppep_preproc" - ], - "Description": "MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/tools-galaxyp/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "mqppep", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep", - "Galaxy wrapper version": "0.1.19", - "Conda id": "bioconductor-preprocesscore", - "Conda version": "1.64.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "msconvert", - "Galaxy tool ids": [ - "msconvert" - ], - "Description": "msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container", - "bio.tool id": "msconvert", - "bio.tool ids": [ - "msconvert" - ], - "biii": null, - "bio.tool name": "msConvert", - "bio.tool description": "msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.", - "EDAM operation": [ - "Filtering", - "Formatting" - ], - "EDAM topic": [ - "Proteomics", - "Proteomics experiment" - ], - "Status": "To update", - "Source": "http://proteowizard.sourceforge.net/tools.shtml", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "msconvert", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", - "Galaxy wrapper version": "3.0.20287", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Filtering", - "Formatting" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Proteomics experiment" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "msgfplus", - "Galaxy tool ids": [ - "msgfplus" - ], - "Description": "MSGF+", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "msgfplus", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus", - "Galaxy wrapper version": "0.5", - "Conda id": "msgf_plus", - "Conda version": "2024.03.26", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "msms_extractor", - "Galaxy tool ids": [ - "msms_extractor" - ], - "Description": "Extract MS/MS scans from the mzML file(s) based on PSM report.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "msms_extractor", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor", - "Galaxy wrapper version": "1.0.0", - "Conda id": "proteowizard", - "Conda version": "3_0_9992", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "msstats", - "Galaxy tool ids": [ - "msstats" - ], - "Description": "MSstats tool for analyzing mass spectrometry proteomic datasets", - "bio.tool id": "msstatstmt", - "bio.tool ids": [ - "msstatstmt" - ], - "biii": null, - "bio.tool name": "MSstatsTMT", - "bio.tool description": "Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", - "EDAM operation": [ - "Spectrum calculation", - "Tag-based peptide identification", - "Differential protein expression profiling" - ], - "EDAM topic": [ - "Proteomics", - "Proteomics experiment", - "Protein expression" - ], - "Status": "To update", - "Source": "https://github.com/MeenaChoi/MSstats", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats", - "Galaxy wrapper version": "4.0.0", - "Conda id": "bioconductor-msstats", - "Conda version": "4.10.0", - "EDAM operation (no superclasses)": [ - "Spectrum calculation", - "Tag-based peptide identification", - "Differential protein expression profiling" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Proteomics experiment", - "Protein expression" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "msstatstmt", - "Galaxy tool ids": [ - "msstatstmt" - ], - "Description": "MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://msstats.org/msstatstmt/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "msstatstmt", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt", - "Galaxy wrapper version": "2.0.0", - "Conda id": "bioconductor-msstatstmt", - "Conda version": "2.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mt2mq", - "Galaxy tool ids": [ - "mt2mq" - ], - "Description": "Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "mt2mq", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq", - "Galaxy wrapper version": "1.1.0", - "Conda id": "r-tidyverse", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mz_to_sqlite", - "Galaxy tool ids": [ - "mz_to_sqlite" - ], - "Description": "Creates a SQLite database for proteomics data", - "bio.tool id": "mztosqlite", - "bio.tool ids": [ - "mztosqlite" - ], - "biii": null, - "bio.tool name": "mzToSQLite", - "bio.tool description": "Convert proteomics data files into a SQLite database", - "EDAM operation": [ - "Conversion", - "Peptide database search" - ], - "EDAM topic": [ - "Proteomics", - "Biological databases" - ], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/mzToSQLite", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "mz_to_sqlite", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite", - "Galaxy wrapper version": "2.1.1+galaxy0", - "Conda id": "mztosqlite", - "Conda version": "2.1.1", - "EDAM operation (no superclasses)": [ - "Conversion", - "Peptide database search" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Biological databases" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "openms", - "Galaxy tool ids": [ - "AccurateMassSearch", - "AssayGeneratorMetabo", - "BaselineFilter", - "CVInspector", - "ClusterMassTraces", - "ClusterMassTracesByPrecursor", - "CometAdapter", - "CompNovo", - "CompNovoCID", - "ConsensusID", - "ConsensusMapNormalizer", - "CruxAdapter", - "DTAExtractor", - "DatabaseFilter", - "DatabaseSuitability", - "DeMeanderize", - "Decharger", - "DecoyDatabase", - "Digestor", - "DigestorMotif", - "EICExtractor", - "ERPairFinder", - "Epifany", - "ExternalCalibration", - "FFEval", - "FalseDiscoveryRate", - "FeatureFinderCentroided", - "FeatureFinderIdentification", - "FeatureFinderIsotopeWavelet", - "FeatureFinderMRM", - "FeatureFinderMetabo", - "FeatureFinderMetaboIdent", - "FeatureFinderMultiplex", - "FeatureLinkerLabeled", - "FeatureLinkerUnlabeled", - "FeatureLinkerUnlabeledKD", - "FeatureLinkerUnlabeledQT", - "FidoAdapter", - "FileConverter", - "FileFilter", - "FileInfo", - "FileMerger", - "FuzzyDiff", - "GNPSExport", - "HighResPrecursorMassCorrector", - "IDConflictResolver", - "IDExtractor", - "IDFileConverter", - "IDFilter", - "IDMapper", - "IDMassAccuracy", - "IDMerger", - "IDPosteriorErrorProbability", - "IDRTCalibration", - "IDRipper", - "IDScoreSwitcher", - "IDSplitter", - "InternalCalibration", - "IsobaricAnalyzer", - "LabeledEval", - "LuciphorAdapter", - "MRMMapper", - "MRMPairFinder", - "MRMTransitionGroupPicker", - "MSFraggerAdapter", - "MSGFPlusAdapter", - "MSSimulator", - "MSstatsConverter", - "MaRaClusterAdapter", - "MapAlignerIdentification", - "MapAlignerPoseClustering", - "MapAlignerSpectrum", - "MapAlignerTreeGuided", - "MapNormalizer", - "MapRTTransformer", - "MapStatistics", - "MascotAdapter", - "MascotAdapterOnline", - "MassCalculator", - "MassTraceExtractor", - "MetaProSIP", - "MetaboliteAdductDecharger", - "MetaboliteSpectralMatcher", - "MultiplexResolver", - "MyriMatchAdapter", - "MzMLSplitter", - "MzTabExporter", - "NoiseFilterGaussian", - "NoiseFilterSGolay", - "NovorAdapter", - "NucleicAcidSearchEngine", - "OMSSAAdapter", - "OpenMSDatabasesInfo", - "OpenPepXL", - "OpenPepXLLF", - "OpenSwathAnalyzer", - "OpenSwathAssayGenerator", - "OpenSwathChromatogramExtractor", - "OpenSwathConfidenceScoring", - "OpenSwathDIAPreScoring", - "OpenSwathDecoyGenerator", - "OpenSwathFeatureXMLToTSV", - "OpenSwathFileSplitter", - "OpenSwathMzMLFileCacher", - "OpenSwathRTNormalizer", - "OpenSwathRewriteToFeatureXML", - "OpenSwathWorkflow", - "PSMFeatureExtractor", - "PTModel", - "PeakPickerHiRes", - "PeakPickerIterative", - "PeakPickerWavelet", - "PepNovoAdapter", - "PeptideIndexer", - "PercolatorAdapter", - "PhosphoScoring", - "PrecursorIonSelector", - "PrecursorMassCorrector", - "ProteinInference", - "ProteinQuantifier", - "ProteinResolver", - "QCCalculator", - "QCEmbedder", - "QCExporter", - "QCExtractor", - "QCImporter", - "QCMerger", - "QCShrinker", - "QualityControl", - "RNADigestor", - "RNAMassCalculator", - "RNPxlSearch", - "RNPxlXICFilter", - "RTEvaluation", - "RTModel", - "SeedListGenerator", - "SemanticValidator", - "SequenceCoverageCalculator", - "SimpleSearchEngine", - "SiriusAdapter", - "SpecLibCreator", - "SpecLibSearcher", - "SpectraFilterBernNorm", - "SpectraFilterMarkerMower", - "SpectraFilterNLargest", - "SpectraFilterNormalizer", - "SpectraFilterParentPeakMower", - "SpectraFilterScaler", - "SpectraFilterSqrtMower", - "SpectraFilterThresholdMower", - "SpectraFilterWindowMower", - "SpectraMerger", - "SpectraSTSearchAdapter", - "StaticModification", - "SvmTheoreticalSpectrumGeneratorTrainer", - "TICCalculator", - "TOFCalibration", - "TargetedFileConverter", - "TextExporter", - "TransformationEvaluation", - "TriqlerConverter", - "XFDR", - "XMLValidator", - "XTandemAdapter" - ], - "Description": "OpenMS Suite for LC/MS data management and analyses", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.openms.de/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "openms", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms", - "Galaxy wrapper version": "2.8", - "Conda id": "openms", - "Conda version": "3.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 8, - "Available on UseGalaxy.org.au": 35, - "Available on UseGalaxy.eu": 160, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pathwaymatcher", - "Galaxy tool ids": [ - "reactome_pathwaymatcher" - ], - "Description": "Reactome Pathway Matcher", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/LuisFranciscoHS/PathwayMatcher", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "reactome_pathwaymatcher", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher", - "Galaxy wrapper version": null, - "Conda id": "pathwaymatcher", - "Conda version": "1.9.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pep_pointer", - "Galaxy tool ids": [ - "pep_pointer" - ], - "Description": "PepPointer categorizes peptides by their genomic coordinates.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Genomic Interval Operations", - "Proteomics" - ], - "ToolShed id": "pep_pointer", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer", - "Galaxy wrapper version": "0.1.3+galaxy1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pepquery", - "Galaxy tool ids": [ - "pepquery" - ], - "Description": "A peptide-centric MS search engine for novel peptide identification and validation.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pepquery.org", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "pepquery", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery", - "Galaxy wrapper version": "1.6.2", - "Conda id": "pepquery", - "Conda version": "2.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pepquery2", - "Galaxy tool ids": [ - "pepquery2", - "pepquery2_index", - "pepquery2_show_sets" - ], - "Description": "PepQuery2 peptide-centric MS search for peptide identification and validation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://pepquery.org", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "pepquery2", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2", - "Galaxy wrapper version": "2.0.2", - "Conda id": "pepquery", - "Conda version": "2.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "peptide_genomic_coordinate", - "Galaxy tool ids": [ - "peptide_genomic_coordinate" - ], - "Description": "Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "peptide_genomic_coordinate", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate", - "Galaxy wrapper version": "1.0.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "peptideshaker", - "Galaxy tool ids": [ - "fasta_cli", - "ident_params", - "peptide_shaker", - "search_gui" - ], - "Description": "PeptideShaker and SearchGUI", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://compomics.github.io", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "peptideshaker", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker", - "Galaxy wrapper version": null, - "Conda id": "searchgui", - "Conda version": "4.3.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "pepxml_to_xls", - "Galaxy tool ids": [], - "Description": "Convert PepXML to Tabular", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "pepxml_to_xls", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "percolator", - "Galaxy tool ids": [ - "batched_set_list_creator", - "percolator", - "percolator_input_converters", - "pout2mzid" - ], - "Description": "Percolator", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "percolator", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator", - "Galaxy wrapper version": "3.5", - "Conda id": "percolator", - "Conda version": "3.6.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pi_db_tools", - "Galaxy tool ids": [ - "calc_delta_pi", - "pi_db_split", - "pi_dbspec_align" - ], - "Description": "HiRIEF tools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "hirieftools", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools", - "Galaxy wrapper version": "1.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pmd_fdr", - "Galaxy tool ids": [ - "pmd_fdr" - ], - "Description": "Calculate Precursor Mass Discrepancy (PMD) for MS/MS", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/slhubler/PMD-FDR-for-Galaxy-P", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "pmd_fdr", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr", - "Galaxy wrapper version": "1.4.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "custom_pro_db", - "Galaxy tool ids": [ - "custom_pro_db" - ], - "Description": "CustomProDB", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/customProDB.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "custom_pro_db", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db", - "Galaxy wrapper version": "1.22.0", - "Conda id": "bioconductor-rgalaxy", - "Conda version": "1.37.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "custom_pro_db_annotation_data_manager", - "Galaxy tool ids": [], - "Description": "CustomProDB Annotation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/customProDB.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "custom_pro_db_annotation_data_manager", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "psm2sam", - "Galaxy tool ids": [ - "PSMtoSAM" - ], - "Description": "PSM to SAM", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://bioconductor.org/packages/release/bioc/html/proBAMr.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "psm_to_sam", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam", - "Galaxy wrapper version": "1.3.2.1", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "proteinpilot", - "Galaxy tool ids": [ - "convert_windows_newlines", - "proteinpilot", - "proteinpilot_group_extractor", - "proteinpilot_tabular", - "proteinpilot_xml" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "proteinpilot", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot", - "Galaxy wrapper version": "0.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "retrieve_ensembl_bed", - "Galaxy tool ids": [ - "retrieve_ensembl_bed" - ], - "Description": "Retrieve cDNA features from Ensembl REST API in BED format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rest.ensembl.org/", - "ToolShed categories": [ - "Data Source" - ], - "ToolShed id": "retrieve_ensembl_bed", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed", - "Galaxy wrapper version": "0.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "translate_bed", - "Galaxy tool ids": [ - "translate_bed" - ], - "Description": "Translate BED transcript CDS or cDNA in 3 frames", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://rest.ensembl.org/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "translate_bed", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed", - "Galaxy wrapper version": "0.1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_joinquantpepionswithproteins", - "Galaxy tool ids": [ - "proteomiqon_joinquantpepionswithproteins" - ], - "Description": "The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_joinquantpepionswithproteins", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins", - "Galaxy wrapper version": "0.0.1", - "Conda id": "proteomiqon-joinquantpepionswithproteins", - "Conda version": "0.0.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_labeledproteinquantification", - "Galaxy tool ids": [ - "proteomiqon_labeledproteinquantification" - ], - "Description": "The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_labeledproteinquantification", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification", - "Galaxy wrapper version": "0.0.1", - "Conda id": "proteomiqon-labeledproteinquantification", - "Conda version": "0.0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_labelfreeproteinquantification", - "Galaxy tool ids": [ - "proteomiqon_labelfreeproteinquantification" - ], - "Description": "The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_labelfreeproteinquantification", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification", - "Galaxy wrapper version": "0.0.1", - "Conda id": "proteomiqon-labelfreeproteinquantification", - "Conda version": "0.0.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_mzmltomzlite", - "Galaxy tool ids": [ - "proteomiqon_mzmltomzlite" - ], - "Description": "The tool MzMLToMzLite allows to convert mzML files to mzLite files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_mzmltomzlite", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite", - "Galaxy wrapper version": "0.0.8", - "Conda id": "proteomiqon-mzmltomzlite", - "Conda version": "0.0.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_peptidedb", - "Galaxy tool ids": [ - "proteomiqon_peptidedb" - ], - "Description": "The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_peptidedb", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb", - "Galaxy wrapper version": "0.0.7", - "Conda id": "proteomiqon-peptidedb", - "Conda version": "0.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_peptidespectrummatching", - "Galaxy tool ids": [ - "proteomiqon_peptidespectrummatching" - ], - "Description": "Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_peptidespectrummatching", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching", - "Galaxy wrapper version": "0.0.7", - "Conda id": "proteomiqon-peptidespectrummatching", - "Conda version": "0.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_proteininference", - "Galaxy tool ids": [ - "proteomiqon_proteininference" - ], - "Description": "MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_proteininference", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference", - "Galaxy wrapper version": "0.0.7", - "Conda id": "proteomiqon-proteininference", - "Conda version": "0.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_psmbasedquantification", - "Galaxy tool ids": [ - "proteomiqon_psmbasedquantification" - ], - "Description": "The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_psmbasedquantification", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification", - "Galaxy wrapper version": "0.0.8", - "Conda id": "proteomiqon-psmbasedquantification", - "Conda version": "0.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteomiqon_psmstatistics", - "Galaxy tool ids": [ - "proteomiqon_psmstatistics" - ], - "Description": "The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteomiqon_psmstatistics", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics", - "Galaxy wrapper version": "0.0.8", - "Conda id": "proteomiqon-psmstatistics", - "Conda version": "0.0.8", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "proteore_venn_diagram", - "Galaxy tool ids": [ - "proteore_venn_diagram" - ], - "Description": "ProteoRE JVenn Diagram", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "proteore_venn_diagram", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram", - "Galaxy wrapper version": "2021.06.08", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "protxml_to_xls", - "Galaxy tool ids": [ - "protxml_to_xls" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "protxml_to_xls", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls", - "Galaxy wrapper version": "0.1.0", - "Conda id": "trans_proteomic_pipeline", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "psm_eval", - "Galaxy tool ids": [ - "psm_eval" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "psm_eval", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval", - "Galaxy wrapper version": "0.1.0", - "Conda id": "binaries_for_psm_eval", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "psm_validation", - "Galaxy tool ids": [ - "psmvalidator" - ], - "Description": "Validate PSM from Ion Fragmentation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/psm_fragments.git", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "psm_validation", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation", - "Galaxy wrapper version": "1.0.3", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pyprophet", - "Galaxy tool ids": [ - "pyprophet_export", - "pyprophet_merge", - "pyprophet_peptide", - "pyprophet_protein", - "pyprophet_score", - "pyprophet_subsample" - ], - "Description": "Semi-supervised learning and scoring of OpenSWATH results.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/PyProphet/pyprophet", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet", - "Galaxy wrapper version": "2.1.4", - "Conda id": "pyprophet", - "Conda version": "2.2.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pyteomics", - "Galaxy tool ids": [ - "mztab2tsv" - ], - "Description": "Tools using the pyteomics library", - "bio.tool id": "pyteomics", - "bio.tool ids": [ - "pyteomics" - ], - "biii": null, - "bio.tool name": "Pyteomics", - "bio.tool description": "Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.", - "EDAM operation": [ - "Protein identification" - ], - "EDAM topic": [ - "Proteomics", - "Proteomics experiment" - ], - "Status": "To update", - "Source": "https://pyteomics.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Proteomics", - "Metabolomics" - ], - "ToolShed id": "pyteomics", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics", - "Galaxy wrapper version": "4.4.1", - "Conda id": "pyteomics", - "Conda version": "4.7.2", - "EDAM operation (no superclasses)": [ - "Protein identification" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Proteomics experiment" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "quantp", - "Galaxy tool ids": [ - "quantp" - ], - "Description": "Correlation between protein and transcript abundance", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "quantp", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp", - "Galaxy wrapper version": "1.1.2", - "Conda id": "r-data.table", - "Conda version": "1.11.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "quantwiz_iq", - "Galaxy tool ids": [ - "quantwiz_iq" - ], - "Description": "Isobaric Quantitation using QuantWiz-IQ", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://sourceforge.net/projects/quantwiz/", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "quantwiz_iq", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq", - "Galaxy wrapper version": "2.0", - "Conda id": "quantwiz-iq", - "Conda version": "2.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qupath_roi_splitter", - "Galaxy tool ids": [ - "qupath_roi_splitter" - ], - "Description": "Split ROI coordinates of QuPath TMA annotation by cell type", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/npinter/ROIsplitter", - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "qupath_roi_splitter", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "hhttps://github.com/npinter/ROIsplitter", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter", - "Galaxy wrapper version": "0.2.1", - "Conda id": "geojson", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rawtools", - "Galaxy tool ids": [ - "rawtools" - ], - "Description": "Raw Tools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/kevinkovalchik/RawTools", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "rawtools", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools", - "Galaxy wrapper version": null, - "Conda id": "rawtools", - "Conda version": "2.0.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "regex_find_replace", - "Galaxy tool ids": [ - "regex1", - "regexColumn1" - ], - "Description": "Use python regular expressions to find and replace text", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "regex_find_replace", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace", - "Galaxy wrapper version": "1.0.3", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "scaffold", - "Galaxy tool ids": [ - "scaffold", - "scaffold_export" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [], - "ToolShed id": "scaffold", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold", - "Galaxy wrapper version": "0.1.0", - "Conda id": "scaffold", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sixgill", - "Galaxy tool ids": [ - "sixgill_build", - "sixgill_filter", - "sixgill_makefasta", - "sixgill_merge" - ], - "Description": "Six-frame Genome-Inferred Libraries for LC-MS/MS", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": null, - "ToolShed categories": [ - "Proteomics", - "MetaProteomics" - ], - "ToolShed id": "sixgill", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill", - "Galaxy wrapper version": "0.2.4", - "Conda id": "sixgill", - "Conda version": "0.2.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spectrast2spectrast_irt", - "Galaxy tool ids": [ - "gp_spectrast2spectrast_irt" - ], - "Description": "Filter from spectraST files to swath input files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "spectrast2spectrast_irt", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt", - "Galaxy wrapper version": "0.1.0", - "Conda id": "msproteomicstools", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spectrast2tsv", - "Galaxy tool ids": [ - "gp_spectrast2tsv" - ], - "Description": "Filter from spectraST files to swath input files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "spectrast2tsv", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv", - "Galaxy wrapper version": "0.1.0", - "Conda id": "msproteomicstools", - "Conda version": "0.11.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "translate_bed_sequences", - "Galaxy tool ids": [ - "translate_bed_sequences" - ], - "Description": "Perform 3 frame translation of BED file augmented with a sequence column", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "translate_bed_sequences", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences", - "Galaxy wrapper version": "0.2.0", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "unipept", - "Galaxy tool ids": [ - "unipept" - ], - "Description": "Unipept retrieves metaproteomics information", - "bio.tool id": "unipept", - "bio.tool ids": [ - "unipept" - ], - "biii": null, - "bio.tool name": "Unipept", - "bio.tool description": "Metaproteomics data analysis with a focus on interactive data visualizations.", - "EDAM operation": [ - "Prediction and recognition", - "Visualisation" - ], - "EDAM topic": [ - "Proteomics", - "Proteogenomics", - "Biodiversity", - "Workflows" - ], - "Status": "To update", - "Source": "https://github.com/galaxyproteomics/tools-galaxyp", - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "unipept", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://unipept.ugent.be/apidocs", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept", - "Galaxy wrapper version": "4.5.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Prediction and recognition", - "Visualisation" - ], - "EDAM topic (no superclasses)": [ - "Proteomics", - "Proteogenomics", - "Biodiversity", - "Workflows" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "uniprotxml_downloader", - "Galaxy tool ids": [ - "uniprotxml_downloader" - ], - "Description": "Download UniProt proteome in XML or fasta format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Proteomics" - ], - "ToolShed id": "uniprotxml_downloader", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader", - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader", - "Galaxy wrapper version": "2.4.0", - "Conda id": "requests", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "validate_fasta_database", - "Galaxy tool ids": [ - "validate_fasta_database" - ], - "Description": "runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Fasta Manipulation", - "Proteomics" - ], - "ToolShed id": "validate_fasta_database", - "Galaxy wrapper owner": "galaxyp", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database", - "Galaxy wrapper version": "0.1.5", - "Conda id": "validate-fasta-database", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bio3d", - "Galaxy tool ids": [ - "bio3d_dccm", - "bio3d_pca", - "bio3d_rmsd", - "bio3d_rmsf", - "bio3d_pca_visualize" - ], - "Description": "Bio3d is a program that can be used to analyse molecular dynamics trajectories.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://thegrantlab.org/bio3d/index.php", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "bio3d", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d", - "Galaxy wrapper version": "2.4_1", - "Conda id": "r-bio3d", - "Conda version": "2.3_3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 4, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biomoldyn", - "Galaxy tool ids": [ - "biomd_neqgamma", - "fastpca", - "biomd_extract_clusters", - "biomd_rmsd_clustering" - ], - "Description": "Tools for MD analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/moldyn/", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "biomoldyn", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn", - "Galaxy wrapper version": "1.5.2", - "Conda id": "scipy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ambertools", - "Galaxy tool ids": [ - "ambertools_acpype", - "acpype_Amber2Gromacs", - "ambertools_antechamber", - "mmpbsa_mmgbsa", - "ambertools_parmchk2", - "parmconv", - "tleap" - ], - "Description": "Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://ambermd.org/AmberTools.php", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "ambertools", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools", - "Galaxy wrapper version": "21.10", - "Conda id": "ambertools", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 7, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "packmol", - "Galaxy tool ids": [ - "packmol" - ], - "Description": "PACKMOL is a package for creating starting structures for Molecular Dynamics simulations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://m3g.iqm.unicamp.br/packmol/home.shtml", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "packmol", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol", - "Galaxy wrapper version": "18.169.1", - "Conda id": "packmol", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "topologyeditors", - "Galaxy tool ids": [ - "gromacs_modify_topology", - "gromacs_extract_topology" - ], - "Description": "Set of python scripts and associated tool files that can be used to modify topology files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "topologyeditors", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", - "Galaxy wrapper version": "0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "free_energy", - "Galaxy tool ids": [], - "Description": "Free energy tools of BRIDGE.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "freeenergy", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gromacs", - "Galaxy tool ids": [ - "gmx_check", - "gmx_editconf", - "gmx_energy", - "gmx_get_builtin_file", - "gmx_rg", - "gmx_makendx", - "gmx_merge_topology_files", - "gmx_em", - "gmx_restraints", - "gmx_rmsd", - "gmx_rmsf", - "gmx_setup", - "gmx_sim", - "gmx_solvate", - "gmx_trj" - ], - "Description": "GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/gromacs", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "gromacs", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs", - "Galaxy wrapper version": "2022", - "Conda id": "gromacs", - "Conda version": "2021.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 14, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 15, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mdanalysis", - "Galaxy tool ids": [ - "mdanalysis_angle", - "mdanalysis_dihedral", - "mdanalysis_distance", - "mdanalysis_endtoend", - "mdanalysis_extract_rmsd", - "mdanalysis_hbonds", - "mdanalysis_cosine_analysis", - "mdanalysis_ramachandran_protein", - "mdanalysis_ramachandran_plot", - "mdanalysis_rdf" - ], - "Description": "MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/MDAnalysis/mdanalysis", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "mdanalysis", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis", - "Galaxy wrapper version": "1.0.0", - "Conda id": "mdanalysis", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 10, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 10, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mdfileconverter", - "Galaxy tool ids": [ - "md_converter" - ], - "Description": "A tool for interconverting between different MD structure and trajectory file formats.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "md_converter", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter", - "Galaxy wrapper version": "1.9.7", - "Conda id": "mdtraj", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mdslicer", - "Galaxy tool ids": [ - "md_slicer" - ], - "Description": "A tool for slicing trajectory files using MDTraj.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "md_converter", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer", - "Galaxy wrapper version": "1.9.9", - "Conda id": "mdtraj", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mdtraj", - "Galaxy tool ids": [ - "traj_selections_and_merge" - ], - "Description": "MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/mdtraj/mdtraj", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "mdtraj", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj", - "Galaxy wrapper version": "1.9.7", - "Conda id": "mdtraj", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "openmm", - "Galaxy tool ids": [ - "pdbfixer" - ], - "Description": "OpenMM is a toolkit for molecular simulation using high performance GPU code.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/openmm", - "ToolShed categories": [ - "Molecular Dynamics", - "Computational chemistry" - ], - "ToolShed id": "openmm", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm", - "Galaxy wrapper version": "1.8.1", - "Conda id": "pdbfixer", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vmd", - "Galaxy tool ids": [], - "Description": "vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.ks.uiuc.edu/Research/vmd/", - "ToolShed categories": [ - "Computational chemistry" - ], - "ToolShed id": "vmd", - "Galaxy wrapper owner": "chemteam", - "Galaxy wrapper source": "https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd", - "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "artbio_bam_cleaning", - "Galaxy tool ids": [ - "artbio_bam_cleaning" - ], - "Description": "filter bam files before somatic-varscan or lumpy-smoove analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "SAM", - "Variant Analysis" - ], - "ToolShed id": "artbio_bam_cleaning", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning", - "Galaxy wrapper version": "1.10+galaxy0", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bamparse", - "Galaxy tool ids": [ - "bamparse" - ], - "Description": "Generates hit count lists from bam alignments.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Transcriptomics" - ], - "ToolShed id": "bamparse", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse", - "Galaxy wrapper version": "4.1.1", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bigwig_to_bedgraph", - "Galaxy tool ids": [ - "bigwig_to_bedgraph" - ], - "Description": "Converts a bigWig file to bedGraph format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "bigwig_to_bedgraph", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph", - "Galaxy wrapper version": "377+galaxy1", - "Conda id": "ucsc-bigwigtobedgraph", - "Conda version": "448", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "bigwig_to_wig", - "Galaxy tool ids": [ - "bigwig_to_wig" - ], - "Description": "Converts a bigWig file to Wiggle (WIG) format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://artbio.fr", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "bigwig_to_wig", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig", - "Galaxy wrapper version": "3+galaxy0", - "Conda id": "ucsc-bigwiginfo", - "Conda version": "377", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast_to_scaffold", - "Galaxy tool ids": [ - "blast2scaffold" - ], - "Description": "Generate DNA scaffold from blastn or tblastx alignments of Contigs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Sequence Analysis", - "Assembly" - ], - "ToolShed id": "blast_to_scaffold", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold", - "Galaxy wrapper version": "1.1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast_unmatched", - "Galaxy tool ids": [ - "blast_unmatched" - ], - "Description": "Extract unmatched query sequences from blast", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "blast_unmatched", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched", - "Galaxy wrapper version": "1.0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blastparser_and_hits", - "Galaxy tool ids": [ - "BlastParser_and_hits" - ], - "Description": "Parse blast outputs and compile hits", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Assembly", - "RNA" - ], - "ToolShed id": "blastparser_and_hits", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits", - "Galaxy wrapper version": "2.7.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blastx_to_scaffold", - "Galaxy tool ids": [ - "blastx2scaffold" - ], - "Description": "Generate DNA scaffold from blastx alignment of Contigs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Sequence Analysis", - "Assembly" - ], - "ToolShed id": "blastx_to_scaffold", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold", - "Galaxy wrapper version": "1.1.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cap3", - "Galaxy tool ids": [ - "cap3" - ], - "Description": "cap3 wrapper", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Assembly" - ], - "ToolShed id": "cap3", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3", - "Galaxy wrapper version": "2.0.1", - "Conda id": "cap3", - "Conda version": "10.2011", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cherry_pick_fasta", - "Galaxy tool ids": [ - "cherry_pick_fasta" - ], - "Description": "Pick fasta sequence with specific header content", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Fasta Manipulation" - ], - "ToolShed id": "cherry_pick_fasta", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta", - "Galaxy wrapper version": "4.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "concat_multi_datasets", - "Galaxy tool ids": [ - "cat_multi_datasets" - ], - "Description": "Concatenate multiple datasets tail-to-head, including collection datasets.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "concatenate_multiple_datasets", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets", - "Galaxy wrapper version": "1.4.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cpm_tpm_rpk", - "Galaxy tool ids": [ - "cpm_tpm_rpk" - ], - "Description": "Generate CPM,TPM or RPK from raw counts", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "cpm_tpm_rpk", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk", - "Galaxy wrapper version": "0.5.2", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "deseq2_normalization", - "Galaxy tool ids": [ - "deseq2_normalization" - ], - "Description": "Normalizes gene hitlists", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Transcriptomics", - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": "deseq2_normalization", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization", - "Galaxy wrapper version": "1.40.2+galaxy0", - "Conda id": "bioconductor-deseq2", - "Conda version": "1.42.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "embl2fa", - "Galaxy tool ids": [ - "embl2fa" - ], - "Description": "Converts EMBL flat format to fasta format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "embl2fa", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa", - "Galaxy wrapper version": "0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ez_histograms", - "Galaxy tool ids": [ - "ez_histograms" - ], - "Description": "ggplot2 histograms and density plots", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/tidyverse/ggplot2", - "ToolShed categories": [ - "Visualization", - "Statistics" - ], - "ToolShed id": "ez_histograms", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms", - "Galaxy wrapper version": "3.4.4", - "Conda id": "r-ggplot2", - "Conda version": "2.2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fetch_fasta_from_ncbi", - "Galaxy tool ids": [ - "retrieve_fasta_from_NCBI" - ], - "Description": "Fetch fasta sequences from NCBI using eutils wrappers", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Fasta Manipulation", - "Data Source" - ], - "ToolShed id": "fetch_fasta_from_ncbi", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi", - "Galaxy wrapper version": "3.1.0", - "Conda id": "urllib3", - "Conda version": "1.12", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fisher_test", - "Galaxy tool ids": [ - "fishertest" - ], - "Description": "Fisher's exact test on two-column hit lists.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Statistics" - ], - "ToolShed id": "fishertest", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test", - "Galaxy wrapper version": "2.32.0+galaxy0", - "Conda id": "bioconductor-qvalue", - "Conda version": "2.34.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gatk4", - "Galaxy tool ids": [ - "filtermutectcalls", - "mergemutectstats", - "mutect2" - ], - "Description": "Find somatic variations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "gatk4", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4", - "Galaxy wrapper version": "4.1.7.0", - "Conda id": "gatk4", - "Conda version": "4.5.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "get_reference_fasta", - "Galaxy tool ids": [ - "get_fasta_reference" - ], - "Description": "Obtain reference genome sequence.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Data Source", - "Fasta Manipulation" - ], - "ToolShed id": "get_reference_fasta", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta", - "Galaxy wrapper version": "0.3.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_center_scale", - "Galaxy tool ids": [ - "center_scale" - ], - "Description": "Center or scale (standardize) data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Statistics" - ], - "ToolShed id": "gsc_center_scale", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale", - "Galaxy wrapper version": "4.3.1+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_filter_cells", - "Galaxy tool ids": [ - "filter_cells" - ], - "Description": "Filter single cell RNAseq data on libray depth and number of detected genes", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_filter_cells", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells", - "Galaxy wrapper version": "4.3.1+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_filter_genes", - "Galaxy tool ids": [ - "filter_genes" - ], - "Description": "Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_filter_genes", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes", - "Galaxy wrapper version": "4.3.1+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_gene_expression_correlations", - "Galaxy tool ids": [ - "single_cell_gene_expression_correlations" - ], - "Description": "Compute single-cell paire-wise gene expressions correlations", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_gene_expression_correlations", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations", - "Galaxy wrapper version": "4.3.1+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_high_dimensions_visualisation", - "Galaxy tool ids": [ - "high_dimensions_visualisation" - ], - "Description": "Generates PCA, t-SNE and HCPC visualisation", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics", - "Visualization" - ], - "ToolShed id": "gsc_high_dimensions_visualisation", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation", - "Galaxy wrapper version": "4.3+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_mannwhitney_de", - "Galaxy tool ids": [ - "mannwhitney_de" - ], - "Description": "Perform a mann-whitney differential testing between two sets of gene expression data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_mannwhitney_de", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de", - "Galaxy wrapper version": "4.1.3+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_scran_normalize", - "Galaxy tool ids": [ - "scran_normalize" - ], - "Description": "Normalize raw counts using scran", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_scran_normalize", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize", - "Galaxy wrapper version": "1.28.1+galaxy0", - "Conda id": "bioconductor-scran", - "Conda version": "1.30.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gsc_signature_score", - "Galaxy tool ids": [ - "signature_score" - ], - "Description": "Compute signature scores from single cell RNAseq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "gsc_signature_score", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score", - "Galaxy wrapper version": "2.3.9+galaxy0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "guppy", - "Galaxy tool ids": [ - "guppy-basecaller" - ], - "Description": "A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "guppy_basecaller", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", - "Galaxy wrapper version": "0.2.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "high_dim_heatmap", - "Galaxy tool ids": [ - "high_dim_heatmap" - ], - "Description": "gplot heatmap.2 function adapted for plotting large heatmaps", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/cran/gplots", - "ToolShed categories": [ - "Visualization" - ], - "ToolShed id": "high_dim_heatmap", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap", - "Galaxy wrapper version": "3.1.3+galaxy0", - "Conda id": "r-gplots", - "Conda version": "2.17.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "justdiff", - "Galaxy tool ids": [ - "justdiff" - ], - "Description": "Unix diff", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "justdiff", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff", - "Galaxy wrapper version": "3.10+galaxy0", - "Conda id": "diffutils", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "justgzip", - "Galaxy tool ids": [ - "justgzip" - ], - "Description": "Compress fastq sequence files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "justgzip", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip", - "Galaxy wrapper version": "2.8+galaxy0", - "Conda id": "pigz", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "lumpy_smoove", - "Galaxy tool ids": [ - "lumpy_smoove", - "vcf2hrdetect" - ], - "Description": "Galaxy wrapper of the lumpy-using smoove workflow", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "lumpy_smoove", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove", - "Galaxy wrapper version": "0.2.8+galaxy1", - "Conda id": "svtyper", - "Conda version": "0.7.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "manta", - "Galaxy tool ids": [ - "manta" - ], - "Description": "Structural variant and indel caller for mapped sequencing data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "manta", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/manta", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/manta", - "Galaxy wrapper version": "1.6", - "Conda id": "manta", - "Conda version": "1.6.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mapping_quality_stats", - "Galaxy tool ids": [ - "mapqstatistics" - ], - "Description": "Collects and shows the distribution of MAPQ values in a BAM alignment file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Sequence Analysis", - "Statistics" - ], - "ToolShed id": "mapping_quality_stats", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats", - "Galaxy wrapper version": "0.22.0", - "Conda id": "r-optparse", - "Conda version": "1.3.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mircounts", - "Galaxy tool ids": [ - "mircounts" - ], - "Description": "Generates miRNA count lists from read alignments to mirBase.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Transcriptomics" - ], - "ToolShed id": "mircounts", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts", - "Galaxy wrapper version": "1.6", - "Conda id": "tar", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mutational_patterns", - "Galaxy tool ids": [ - "mutational_patterns" - ], - "Description": "Mutational patterns and signatures in base substitution catalogs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "mutational_patterns", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns", - "Galaxy wrapper version": "3.12.0", - "Conda id": "bioconductor-mutationalpatterns", - "Conda version": "3.12.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "oases", - "Galaxy tool ids": [ - "oasesoptimiserv" - ], - "Description": "Short read assembler", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Assembly", - "RNA" - ], - "ToolShed id": "oases", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/oases", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/oases", - "Galaxy wrapper version": "1.4.0", - "Conda id": "oases", - "Conda version": "0.2.09", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pathifier", - "Galaxy tool ids": [ - "pathifier" - ], - "Description": "pathifier", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://", - "ToolShed categories": [ - "Transcriptomics", - "Statistics" - ], - "ToolShed id": "pathifier", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier", - "Galaxy wrapper version": "1.40.0", - "Conda id": "bioconductor-pathifier", - "Conda version": "1.40.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "pindel", - "Galaxy tool ids": [ - "pindel" - ], - "Description": "Pindel detects genome-wide structural variation.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "pindel", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel", - "Galaxy wrapper version": "0.2.5b9", - "Conda id": "pindel", - "Conda version": "0.2.5b9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "probecoverage", - "Galaxy tool ids": [ - "probecoverage" - ], - "Description": "computes and plots read coverage of genomic regions by sequencing datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Sequence Analysis", - "Genomic Interval Operations", - "Graphics", - "Statistics" - ], - "ToolShed id": "probecoverage", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage", - "Galaxy wrapper version": "0.22.0", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "repenrich", - "Galaxy tool ids": [ - "edger-repenrich", - "repenrich" - ], - "Description": "Repeat element profiling", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "repenrich", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", - "Galaxy wrapper version": "2.31.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "repenrich2", - "Galaxy tool ids": [ - "edger-repenrich2", - "repenrich2" - ], - "Description": "Repeat element profiling using bowtie2 aligner", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "repenrich2", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", - "Galaxy wrapper version": "2.31.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rsem", - "Galaxy tool ids": [ - "extract_transcript_to_gene_map_from_trinity", - "purgegtffrommultichromgenes", - "rsembowtie2", - "rsembowtie" - ], - "Description": "transcript quantification from RNA-Seq data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/deweylab/RSEM", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": "rsem", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/master/tools/rsem", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem", - "Galaxy wrapper version": null, - "Conda id": "rsem", - "Conda version": "1.3.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sambamba", - "Galaxy tool ids": [ - "sambamba_sample_or_filter" - ], - "Description": "filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "sambamba", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba", - "Galaxy wrapper version": "0.7.1+galaxy1", - "Conda id": "sambamba", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sashimi_plot", - "Galaxy tool ids": [ - "sashimi_plot" - ], - "Description": "Generates a sashimi plot from bam files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Transcriptomics", - "Graphics", - "Visualization" - ], - "ToolShed id": "sashimi_plot", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot", - "Galaxy wrapper version": "0.1.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sequence_format_converter", - "Galaxy tool ids": [ - "sequence_format_converter" - ], - "Description": "various fasta to tabular conversions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Convert Formats", - "Fasta Manipulation" - ], - "ToolShed id": "sequence_format_converter", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter", - "Galaxy wrapper version": "2.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "small_rna_clusters", - "Galaxy tool ids": [ - "small_rna_clusters" - ], - "Description": "clusters small rna reads in alignment BAM files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "SAM", - "Graphics", - "Next Gen Mappers" - ], - "ToolShed id": "small_rna_clusters", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters", - "Galaxy wrapper version": "1.3.0", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "small_rna_maps", - "Galaxy tool ids": [ - "small_rna_maps" - ], - "Description": "Generates small read maps from alignment BAM files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "SAM", - "Graphics", - "Next Gen Mappers" - ], - "ToolShed id": "small_rna_maps", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps", - "Galaxy wrapper version": "3.1.1", - "Conda id": "numpy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "small_rna_signatures", - "Galaxy tool ids": [ - "overlapping_reads", - "signature" - ], - "Description": "Computes the tendency of small RNAs to overlap with each other.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "small_rna_signatures", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures", - "Galaxy wrapper version": "3.4.2", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snvtocnv", - "Galaxy tool ids": [ - "sequenzaindex", - "snvtocnv" - ], - "Description": "infer copy number variations from a vcf file with SNVs using R sequenza", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "snvtocnv", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv", - "Galaxy wrapper version": "3.0.0+galaxy1", - "Conda id": "sequenza-utils", - "Conda version": "3.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sr_bowtie", - "Galaxy tool ids": [ - "bowtieForSmallRNA" - ], - "Description": "bowtie wrapper tool to align small RNA sequencing reads", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Next Gen Mappers" - ], - "ToolShed id": "sr_bowtie", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie", - "Galaxy wrapper version": "2.3.0", - "Conda id": "bowtie", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sr_bowtie_dataset_annotation", - "Galaxy tool ids": [ - "sr_bowtie_dataset_annotation" - ], - "Description": "Maps iteratively small RNA sequencing datasets to reference sequences.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA" - ], - "ToolShed id": "sr_bowtie_dataset_annotation", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation", - "Galaxy wrapper version": "2.8", - "Conda id": "bowtie", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "tarfast5", - "Galaxy tool ids": [ - "tarfast5" - ], - "Description": "produces a tar.gz archive of fast5 sequence files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "tarfast5", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5", - "Galaxy wrapper version": "0.6.1", - "Conda id": "pigz", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "varscan_vaf", - "Galaxy tool ids": [ - "varscan_vaf" - ], - "Description": "Compute variant allele frequency in vcf files generated by varscan.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "varscan_vaf", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf", - "Galaxy wrapper version": "0.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "xpore", - "Galaxy tool ids": [ - "xpore_dataprep", - "xpore_diffmod" - ], - "Description": "Identification and quantification of differential RNA modifications from direct RNA sequencing", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/GoekeLab/xpore", - "ToolShed categories": [ - "Nanopore" - ], - "ToolShed id": "xpore", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore", - "Galaxy wrapper version": "2.1+galaxy0", - "Conda id": "xpore", - "Conda version": "2.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "yac_clipper", - "Galaxy tool ids": [ - "yac" - ], - "Description": "Clips 3' adapters for small RNA sequencing reads.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://artbio.fr", - "ToolShed categories": [ - "RNA", - "Fastq Manipulation" - ], - "ToolShed id": "yac_clipper", - "Galaxy wrapper owner": "artbio", - "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper", - "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper", - "Galaxy wrapper version": "2.5.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "EMLassemblyline", - "Galaxy tool ids": [ - "eal_table_template", - "eal_templates", - "eml2eal", - "entities_template", - "geo_cov_template", - "makeeml", - "raster_template", - "taxo_cov_template", - "vector_template" - ], - "Description": "Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/EDIorg/EMLassemblyline", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "emlassemblyline", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline", - "Galaxy wrapper version": "0.1.1+galaxy0", - "Conda id": "r-emlassemblyline", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 9, - "Available on UseGalaxy.org.fr": 9 - }, - { - "Galaxy wrapper id": "Ecoregionalization_workflow", - "Galaxy tool ids": [ - "ecoregion_brt_analysis", - "ecoregion_GeoNearestNeighbor", - "ecoregion_cluster_estimate", - "ecoregion_clara_cluster", - "ecoregion_eco_map", - "ecoregion_taxa_seeker" - ], - "Description": "Tools to compute ecoregionalization with BRT model predictions and clustering.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/PaulineSGN/Workflow_Galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "ecoregionalization", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow", - "Galaxy wrapper version": "0.1.0+galaxy0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "Geom_mean_workflow", - "Galaxy tool ids": [ - "Map_shp", - "Mean_geom", - "bar_plot" - ], - "Description": "Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "Geometric means (Dead wood)", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow", - "Galaxy wrapper version": "0.1.0+galaxy0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "PAMPA", - "Galaxy tool ids": [ - "pampa_communitymetrics", - "pampa_presabs", - "pampa_glmcomm", - "pampa_glmsp", - "pampa_plotglm" - ], - "Description": "Tools to compute and analyse biodiversity metrics", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "pampa", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/ColineRoyaux/PAMPA-Galaxy", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA", - "Galaxy wrapper version": "0.0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 5, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "ab1_fastq", - "Galaxy tool ids": [ - "ab1_fastq_converter" - ], - "Description": "Tool to convert ab1 files into FASTQ files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "ab1fastq", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq", - "Galaxy wrapper version": "1.20.0", - "Conda id": "bioconductor-sangerseqr", - "Conda version": "1.38.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "aquainfra_importer", - "Galaxy tool ids": [ - "aquainfra_importer" - ], - "Description": "A data source tool for downloading datasets via the AquaINFRA Interaction Platform.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AquaINFRA/galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer", - "Galaxy wrapper version": "1.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "champ_blocs", - "Galaxy tool ids": [ - "cb_dissim", - "cb_ivr", - "cb_div" - ], - "Description": "Compute indicators for turnover boulders fields", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/Marie59/champ_blocs", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs", - "Galaxy wrapper version": "0.0.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 3 - }, - { - "Galaxy wrapper id": "consensus_from_alignments", - "Galaxy tool ids": [ - "aligned_to_consensus" - ], - "Description": "Tool to compute a consensus sequence from several aligned fasta sequences", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "consalign", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments", - "Galaxy wrapper version": "1.0.0", - "Conda id": "r-bioseq", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "data_exploration", - "Galaxy tool ids": [ - "tool_anonymization", - "ecology_homogeneity_normality", - "ecology_beta_diversity", - "ecology_link_between_var", - "ecology_presence_abs_abund", - "ecology_stat_presence_abs" - ], - "Description": "Explore data through multiple statistical tools", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/Marie59/Data_explo_tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration", - "Galaxy wrapper version": "0.0.0", - "Conda id": "r-tangles", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 6 - }, - { - "Galaxy wrapper id": "xarray", - "Galaxy tool ids": [ - "timeseries_extraction", - "xarray_coords_info", - "xarray_mapplot", - "xarray_metadata_info", - "xarray_netcdf2netcdf", - "xarray_select" - ], - "Description": "xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "http://xarray.pydata.org", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray", - "Galaxy wrapper version": "2022.3.0", - "Conda id": "xarray", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 5, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "gdal", - "Galaxy tool ids": [ - "gdal_gdal_merge", - "gdal_gdal_translate", - "gdal_gdaladdo", - "gdal_gdalbuildvrt", - "gdal_gdalinfo", - "gdal_gdalwarp", - "gdal_ogr2ogr", - "gdal_ogrinfo" - ], - "Description": "Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.gdal.org", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "gdal", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal", - "Galaxy wrapper version": "3.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 8 - }, - { - "Galaxy wrapper id": "interpolation", - "Galaxy tool ids": [ - "interpolation_run_idw_interpolation" - ], - "Description": "Run IDW interpolation based on a .csv and .geojson file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AquaINFRA/galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", - "Galaxy wrapper version": "1.0", - "Conda id": "r-getopt", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "medenv", - "Galaxy tool ids": [ - "iabiodiv_smartbiodiv_med_environ" - ], - "Description": "Retrieve environmental data from etopo, cmems and woa", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/jeremyfix/medenv", - "ToolShed categories": [ - "Ecology", - "Data Source" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/jeremyfix/medenv", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv", - "Galaxy wrapper version": "0.1.0", - "Conda id": "pandas", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "obisindicators", - "Galaxy tool ids": [ - "obisindicators", - "obis_data" - ], - "Description": "Compute biodiveristy indicators for marine data from obis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Marie59/obisindicators", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators", - "Galaxy wrapper version": "0.0.2", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "ocean", - "Galaxy tool ids": [ - "argo_getdata" - ], - "Description": "Access, process, visualise oceanographic data for the Earth System", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Marie59/FE-ft-ESG/tree/main/argo", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean", - "Galaxy wrapper version": "0.1.15", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ogcProcess_otb_bandmath", - "Galaxy tool ids": [ - "otb_band_math" - ], - "Description": "Outputs a monoband image which is the result of a mathematical operation on several multi-band images.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AquaINFRA/galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath", - "Galaxy wrapper version": "1.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ogcProcess_otb_meanShiftSmoothing", - "Galaxy tool ids": [ - "otb_mean_shift_smoothing" - ], - "Description": "This application smooths an image using the MeanShift algorithm.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AquaINFRA/galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing", - "Galaxy wrapper version": "1.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "regionalgam", - "Galaxy tool ids": [ - "regionalgam_ab_index", - "regionalgam_autocor_acf", - "regionalgam_flight_curve", - "regionalgam_glmmpql", - "regionalgam_gls_adjusted", - "regionalgam_gls", - "regionalgam_plot_trend" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RetoSchmucki/regionalGAM", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam", - "Galaxy wrapper version": "1.5", - "Conda id": "r-mgcv", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 7 - }, - { - "Galaxy wrapper id": "sdmpredictors", - "Galaxy tool ids": [ - "sdmpredictors_list_layers" - ], - "Description": "Terrestrial and marine predictors for species distribution modelling.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cran.r-project.org/web/packages/sdmpredictors/index.html", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "sdmpredictors", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors", - "Galaxy wrapper version": "0.2.15", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "spocc", - "Galaxy tool ids": [ - "spocc_occ" - ], - "Description": "Get species occurences data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cran.r-project.org/web/packages/spocc/index.html", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "spocc_occ", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc", - "Galaxy wrapper version": "1.2.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "srs_tools", - "Galaxy tool ids": [ - "srs_diversity_maps", - "srs_global_indices", - "srs_process_data", - "srs_spectral_indices", - "srs_pca", - "srs_preprocess_s2", - "srs_metadata" - ], - "Description": "Compute biodiversity indicators for remote sensing data from Sentinel 2", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/Marie59/Sentinel_2A/srs_tools", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools", - "Galaxy wrapper version": "0.0.1", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 7 - }, - { - "Galaxy wrapper id": "stoc", - "Galaxy tool ids": [ - "stoceps_filteringsp", - "stoceps_glm", - "stoceps_glm_group", - "stoceps_maketablecarrer", - "stoceps_trend_indic" - ], - "Description": "Tools to analyse STOC data.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "stoceps", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc", - "Galaxy wrapper version": "0.0.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 5 - }, - { - "Galaxy wrapper id": "vigiechiro", - "Galaxy tool ids": [ - "vigiechiro_bilanenrichipf", - "vigiechiro_bilanenrichirp", - "vigiechiro_idcorrect_2ndlayer", - "vigiechiro_idvalid" - ], - "Description": "Tools created by the vigiechiro team to analyses and identify chiro sounds files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": "vigiechiro", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro", - "Galaxy wrapper version": "0.1.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 4 - }, - { - "Galaxy wrapper id": "xmlstarlet", - "Galaxy tool ids": [ - "xmlstarlet" - ], - "Description": "Tool to convert a xml file from one metadata standard to another", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "xmlstarlet", - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet", - "Galaxy wrapper version": "1.6.1", - "Conda id": "xmlstarlet", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "zoo_project_ogc_api_processes", - "Galaxy tool ids": [ - "zoo_project_ogc_api_processes" - ], - "Description": "This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/AquaINFRA/galaxy", - "ToolShed categories": [ - "Ecology" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "ecology", - "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper", - "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes", - "Galaxy wrapper version": "0.1.0", - "Conda id": "r-base", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "c3s", - "Galaxy tool ids": [ - "c3s" - ], - "Description": "Copernicus Climate Change Service (C3S)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "c3s", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s", - "Galaxy wrapper version": "0.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cads", - "Galaxy tool ids": [ - "cads" - ], - "Description": "Copernicus Atmosphere Data Store (ADS)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://ads.atmosphere.copernicus.eu/#!/home", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "cads", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads", - "Galaxy wrapper version": "0.1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cdo", - "Galaxy tool ids": [ - "cdo_info", - "cdo_operations" - ], - "Description": "CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://code.mpimet.mpg.de/projects/cdo/", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo", - "Galaxy wrapper version": "2.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cesm", - "Galaxy tool ids": [ - "cesm" - ], - "Description": "Community Earth System Model (CESM)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://www.cesm.ucar.edu/", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "cesm", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/ESCOMP/CESM", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm", - "Galaxy wrapper version": "2.1.3", - "Conda id": "cesm", - "Conda version": "2.1.3", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "climate-stripes", - "Galaxy tool ids": [ - "climate_stripes" - ], - "Description": "Create climate stripes from a tabular input file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://www.climate-lab-book.ac.uk/2018/warming-stripes/", - "ToolShed categories": [ - "Climate Analysis", - "Visualization" - ], - "ToolShed id": "climate_stripes", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes", - "Galaxy wrapper version": "1.0.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "eodie", - "Galaxy tool ids": [ - "eodie" - ], - "Description": "Earth Observation Data Information Extractor", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://eodie.readthedocs.io/", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "eodie", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://gitlab.com/eetun-tiimi/EODIE", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie", - "Galaxy wrapper version": "1.0.2", - "Conda id": "eodie", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "essential_climate_variables", - "Galaxy tool ids": [ - "cds_essential_variability" - ], - "Description": "Get Copernicus Essential Climate Variables for assessing climate variability", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview", - "ToolShed categories": [ - "Climate Analysis", - "Data Source" - ], - "ToolShed id": "cds_essential_variability", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables", - "Galaxy wrapper version": "0.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fates-emerald", - "Galaxy tool ids": [ - "ctsm_fates" - ], - "Description": "EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "ctsm_fates", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald", - "Galaxy wrapper version": "2.0", - "Conda id": "fates-emerald", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mean-per-zone", - "Galaxy tool ids": [ - "mean_per_zone" - ], - "Description": "Creates a png image showing statistic over areas as defined in the vector file", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/", - "ToolShed categories": [ - "Visualization", - "GIS", - "Climate Analysis" - ], - "ToolShed id": "mean_per_zone", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone", - "Galaxy wrapper version": "0.2.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "psy-maps", - "Galaxy tool ids": [ - "psy_maps" - ], - "Description": "Visualization of regular geographical data on a map with psyplot", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/Chilipp/psy-maps", - "ToolShed categories": [ - "Visualization", - "Climate Analysis" - ], - "ToolShed id": "psy_maps", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps", - "Galaxy wrapper version": "1.2.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "shift-longitudes", - "Galaxy tool ids": [ - "shyft_longitudes" - ], - "Description": "Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/", - "ToolShed categories": [ - "Climate Analysis" - ], - "ToolShed id": "shift_longitudes", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes", - "Galaxy wrapper version": "0.1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "smithsonian-volcanoes", - "Galaxy tool ids": [ - "smithsonian_volcanoes" - ], - "Description": "Retrieve data from Volcanoes of the World (VOTW) Database", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://volcano.si.edu/gvp_votw.cfm", - "ToolShed categories": [ - "Retrieve Data" - ], - "ToolShed id": "smithsonian_volcanoes", - "Galaxy wrapper owner": "climate", - "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes", - "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes", - "Galaxy wrapper version": "0.1.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "droplet-barcode-plot", - "Galaxy tool ids": [ - "_dropletBarcodePlot" - ], - "Description": "Make a cell barcode plot for droplet single-cell RNA-seq QC", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "droplet_barcode_plot", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot", - "Galaxy wrapper version": "1.6.1+galaxy2", - "Conda id": "scxa-plots", - "Conda version": "0.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_provider", - "Galaxy tool ids": [ - "fastq_provider" - ], - "Description": "Retrieval and download of FASTQ files from ENA and other repositories such as HCA.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ebi-gene-expression-group/atlas-fastq-provider", - "ToolShed categories": [ - "Data Source", - "RNA", - "Transcriptomics" - ], - "ToolShed id": "atlas_fastq_provider", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider", - "Galaxy wrapper version": "0.4.4", - "Conda id": "atlas-fastq-provider", - "Conda version": "0.4.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gtf-2-gene-list", - "Galaxy tool ids": [ - "_ensembl_gtf2gene_list" - ], - "Description": "Utility to extract annotations from Ensembl GTF files.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "gtf2gene_list", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list", - "Galaxy wrapper version": "1.52.0+galaxy0", - "Conda id": "atlas-gene-annotation-manipulation", - "Conda version": "1.1.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_pair", - "Galaxy tool ids": [ - "fastq_pair" - ], - "Description": "Paired-end fastq pairer", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/linsalrob/fastq-pair", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_pair", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair", - "Galaxy wrapper version": "1.0+galaxy0", - "Conda id": "fastq-pair", - "Conda version": "1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_quality_trimmer", - "Galaxy tool ids": [ - "cshl_fastq_quality_trimmer" - ], - "Description": "FASTQ trimmer based on quality", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/agordon/fastx_toolkit", - "ToolShed categories": [ - "Fastq Manipulation" - ], - "ToolShed id": "fastq_quality_trimmer", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer", - "Galaxy wrapper version": "0.0.14+galaxy0", - "Conda id": "fastx_toolkit", - "Conda version": "0.0.14", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fastq_utils", - "Galaxy tool ids": [ - "fastq_filter_n", - "fastq_trim_poly_at" - ], - "Description": "Set of tools for handling fastq files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/nunofonseca/fastq_utils", - "ToolShed categories": [ - "Transcriptomics", - "RNA" - ], - "ToolShed id": "fastq_utils", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils", - "Galaxy wrapper version": "0.25.1+galaxy0", - "Conda id": "fastq_utils", - "Conda version": "0.25.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "salmon-kallisto-mtx-to-10x", - "Galaxy tool ids": [ - "_salmon_kallisto_mtx_to_10x" - ], - "Description": "Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "salmon_kallisto_mtx_to_10x", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x", - "Galaxy wrapper version": "0.0.1+galaxy6", - "Conda id": "scipy", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cell-types-analysis", - "Galaxy tool ids": [ - "ct_build_cell_ontology_dict", - "ct_check_labels", - "ct_combine_tool_outputs", - "ct_downsample_cells", - "ct_get_consensus_outputs", - "ct_get_empirical_dist", - "ct_get_tool_perf_table", - "ct_get_tool_pvals" - ], - "Description": "Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics" - ], - "ToolShed id": "suite_cell_types_analysis", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis", - "Galaxy wrapper version": "1.1.1", - "Conda id": "cell-types-analysis", - "Conda version": "0.1.11", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "data-hca", - "Galaxy tool ids": [ - "hca_matrix_downloader" - ], - "Description": "Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "suite_human_cell_atlas_tools", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca", - "Galaxy wrapper version": "v0.0.4+galaxy0", - "Conda id": "hca-matrix-downloader", - "Conda version": "0.0.4", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "data-scxa", - "Galaxy tool ids": [ - "retrieve_scxa" - ], - "Description": "Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis" - ], - "ToolShed id": "suite_ebi_expression_atlas", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa", - "Galaxy wrapper version": "v0.0.2+galaxy2", - "Conda id": "wget", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "decoupler", - "Galaxy tool ids": [ - "score_genes_aucell", - "decoupler_pathway_inference", - "decoupler_pseudobulk" - ], - "Description": "decoupler - Ensemble of methods to infer biological activities", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://decoupler-py.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "suite_decoupler", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler", - "Galaxy wrapper version": "1.4.0+galaxy3", - "Conda id": "decoupler", - "Conda version": "1.5.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "dropletutils", - "Galaxy tool ids": [ - "dropletutils_empty_drops", - "dropletutils_read_10x" - ], - "Description": "De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_dropletutils", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils", - "Galaxy wrapper version": "1.0.4", - "Conda id": "dropletutils-scripts", - "Conda version": "0.0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "garnett", - "Galaxy tool ids": [ - "garnett_check_markers", - "garnett_classify_cells", - "garnett_get_feature_genes", - "garnett_get_std_output", - "garnett_train_classifier", - "garnett_transform_markers", - "update_marker_file" - ], - "Description": "De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_garnett", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett", - "Galaxy wrapper version": "0.2.8", - "Conda id": "garnett-cli", - "Conda version": "0.0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "monocle3", - "Galaxy tool ids": [ - "monocle3_create", - "monocle3_diffExp", - "monocle3_learnGraph", - "monocle3_orderCells", - "monocle3_partition", - "monocle3_plotCells", - "monocle3_preprocess", - "monocle3_reduceDim", - "monocle3_topmarkers" - ], - "Description": "De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_monocle3", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3", - "Galaxy wrapper version": "0.1.4", - "Conda id": "monocle3-cli", - "Conda version": "0.0.9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 9, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 9, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sc3", - "Galaxy tool ids": [ - "sc3_calc_biology", - "sc3_calc_consens", - "sc3_calc_dists", - "sc3_calc_transfs", - "sc3_estimate_k", - "sc3_kmeans", - "sc3_prepare" - ], - "Description": "De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_sc3", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3", - "Galaxy wrapper version": "1.8.0", - "Conda id": "sc3-scripts", - "Conda version": "0.0.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scanpy", - "Galaxy tool ids": [ - "anndata_ops", - "scanpy_filter_cells", - "scanpy_filter_genes", - "scanpy_find_cluster", - "scanpy_find_markers", - "scanpy_find_variable_genes", - "scanpy_integrate_bbknn", - "scanpy_integrate_combat", - "scanpy_integrate_harmony", - "scanpy_integrate_mnn", - "scanpy_plot_scrublet", - "scanpy_multiplet_scrublet", - "scanpy_compute_graph", - "scanpy_normalise_data", - "scanpy_parameter_iterator", - "scanpy_plot_embed", - "scanpy_plot_trajectory", - "scanpy_read_10x", - "scanpy_regress_variable", - "scanpy_run_diffmap", - "scanpy_run_dpt", - "scanpy_run_fdg", - "scanpy_run_paga", - "scanpy_run_pca", - "scanpy_run_tsne", - "scanpy_run_umap", - "scanpy_scale_data" - ], - "Description": "scanpy-scripts, command-line wrapper scripts around Scanpy.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://scanpy.readthedocs.io", - "ToolShed categories": [ - "Transcriptomics", - "Sequence Analysis", - "RNA" - ], - "ToolShed id": "scanpy_scripts", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy", - "Galaxy wrapper version": "1.9.3", - "Conda id": "scanpy-scripts", - "Conda version": "1.9.301", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 17, - "Available on UseGalaxy.org.au": 27, - "Available on UseGalaxy.eu": 27, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scater", - "Galaxy tool ids": [ - "scater_calculate_cpm", - "scater_calculate_qc_metrics", - "scater_filter", - "scater_is_outlier", - "scater_normalize", - "scater_read_10x_results" - ], - "Description": "De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_scater", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater", - "Galaxy wrapper version": "1.10.0", - "Conda id": "scater-scripts", - "Conda version": "0.0.5", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 6, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sccaf", - "Galaxy tool ids": [ - "run_sccaf", - "sccaf_asses", - "sccaf_asses_merger", - "sccaf_regress_out" - ], - "Description": "SCCAF: Single Cell Clustering Assessment Framework.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/sccaf/sccaf", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "SCCAF", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf", - "Galaxy wrapper version": "0.0.9", - "Conda id": "sccaf", - "Conda version": "0.0.10", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "sceasy", - "Galaxy tool ids": [ - "sceasy_convert" - ], - "Description": "Convert scRNA data object between popular formats", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "sceasy", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy", - "Galaxy wrapper version": "0.0.5", - "Conda id": "r-sceasy", - "Conda version": "0.0.7", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scmap", - "Galaxy tool ids": [ - "scmap_get_std_output", - "scmap_index_cell", - "scmap_index_cluster", - "scmap_preprocess_sce", - "scmap_scmap_cell", - "scmap_scmap_cluster", - "scmap_select_features" - ], - "Description": "De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_scmap", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap", - "Galaxy wrapper version": "1.6.4", - "Conda id": "scmap-cli", - "Conda version": "0.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 7, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "scpred", - "Galaxy tool ids": [ - "scpred_get_feature_space", - "scpred_get_std_output", - "scpred_predict_labels", - "scpred_train_model" - ], - "Description": "De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_scpred", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred", - "Galaxy wrapper version": "1.0.2", - "Conda id": "scpred-cli", - "Conda version": "0.1.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 4, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "seurat", - "Galaxy tool ids": [ - "seurat_convert", - "seurat_dim_plot", - "seurat_export_cellbrowser", - "seurat_filter_cells", - "seurat_find_clusters", - "seurat_find_markers", - "seurat_find_neighbours", - "seurat_find_variable_genes", - "seurat_hover_locator", - "seurat_integration", - "seurat_map_query", - "seurat_normalise_data", - "seurat_plot", - "seurat_read10x", - "seurat_run_pca", - "seurat_run_tsne", - "seurat_run_umap", - "seurat_scale_data", - "seurat_select_integration_features" - ], - "Description": "De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", - "ToolShed categories": [ - "Transcriptomics", - "RNA", - "Statistics", - "Sequence Analysis" - ], - "ToolShed id": "suite_seurat", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat", - "Galaxy wrapper version": "4.0.0", - "Conda id": "seurat-scripts", - "Conda version": "4.0.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 14, - "Available on UseGalaxy.org.fr": 11 - }, - { - "Galaxy wrapper id": "ucsc-cell-browser", - "Galaxy tool ids": [ - "ucsc_cell_browser" - ], - "Description": "Python pipeline and Javascript scatter plot library for single-cell datasets", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://cells.ucsc.edu/", - "ToolShed categories": [ - "Transcriptomics" - ], - "ToolShed id": "ucsc_cell_browser", - "Galaxy wrapper owner": "ebi-gxa", - "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml", - "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser", - "Galaxy wrapper version": "1.0.0+galaxy1", - "Conda id": "ucsc-cell-browser", - "Conda version": "1.2.6", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "biotransformer", - "Galaxy tool ids": [ - "biotransformer" - ], - "Description": "BioTransformer is a tool for prediction of small molecule metabolism in mammals.", - "bio.tool id": "biotransformer", - "bio.tool ids": [ - "biotransformer" - ], - "biii": null, - "bio.tool name": "BioTransformer", - "bio.tool description": "BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.", - "EDAM operation": [ - "Metabolic pathway prediction", - "PTM site prediction", - "Natural product identification" - ], - "EDAM topic": [ - "Small molecules", - "Endocrinology and metabolism", - "Metabolomics", - "Carbohydrates", - "NMR" - ], - "Status": "Up-to-date", - "Source": "https://bitbucket.org/djoumbou/biotransformerjar/src/master/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "biotransformer", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer", - "Galaxy wrapper version": "3.0.20230403", - "Conda id": "biotransformer", - "Conda version": "3.0.20230403", - "EDAM operation (no superclasses)": [ - "Metabolic pathway prediction", - "PTM site prediction", - "Natural product identification" - ], - "EDAM topic (no superclasses)": [ - "Small molecules", - "Endocrinology and metabolism", - "Metabolomics", - "Carbohydrates", - "NMR" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "filter_compounds", - "Galaxy tool ids": [ - "filter_orgmet_anorg" - ], - "Description": "Tool for filtering organometallics/anorganic compounds from a list of compounds.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "filter_compounds", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds", - "Galaxy wrapper version": "3.1.1", - "Conda id": "openbabel", - "Conda version": "2.3.90dev7d621d9", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "gc_derivatization", - "Galaxy tool ids": [ - "gc_derivatization" - ], - "Description": "In silico derivatization for GC.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/gc-meox-tms", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "gc_derivatization", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization", - "Galaxy wrapper version": "1.0.1", - "Conda id": "gc-meox-tms", - "Conda version": "1.0.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "isolib", - "Galaxy tool ids": [ - "isolib" - ], - "Description": "Create an isotopic pattern library for given compounds and adducts.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "isolib", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/isolib", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/isolib", - "Galaxy wrapper version": "1.0.1+galaxy0", - "Conda id": "bioconductor-metabocoreutils", - "Conda version": "1.10.0", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "matchms", - "Galaxy tool ids": [ - "matchms_add_key", - "matchms_convert", - "matchms_filtering", - "matchms_fingerprint_similarity", - "matchms_formatter", - "matchms_metadata_export", - "matchms_metadata_match", - "matchms_metadata_merge", - "matchms_networking", - "matchms_remove_key", - "matchms_remove_spectra", - "matchms_spectral_similarity", - "matchms_split", - "matchms_subsetting" - ], - "Description": "Searching, filtering and converting mass spectral libraries.", - "bio.tool id": "matchms", - "bio.tool ids": [ - "matchms" - ], - "biii": null, - "bio.tool name": "Matchms", - "bio.tool description": "Tool to import, process, clean, and compare mass spectrometry data.", - "EDAM operation": [ - "Spectral library search", - "Format validation", - "Filtering" - ], - "EDAM topic": [ - "Metabolomics" - ], - "Status": "To update", - "Source": "https://github.com/matchms/matchms", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "matchms", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/matchms", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/matchms", - "Galaxy wrapper version": "0.25.0", - "Conda id": "matchms", - "Conda version": "0.26.2", - "EDAM operation (no superclasses)": [ - "Spectral library search", - "Format validation", - "Filtering" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 9, - "Available on UseGalaxy.eu": 14, - "Available on UseGalaxy.org.fr": 11 - }, - { - "Galaxy wrapper id": "misc", - "Galaxy tool ids": [ - "use_theoretical_mz_annotations" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc", - "Galaxy wrapper version": "1.0.0", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "msmetaenhancer", - "Galaxy tool ids": [ - "msmetaenhancer" - ], - "Description": null, - "bio.tool id": "msmetaenhancer", - "bio.tool ids": [ - "msmetaenhancer" - ], - "biii": null, - "bio.tool name": "MSMetaEnhancer", - "bio.tool description": "Tool for mass spectra metadata annotation.", - "EDAM operation": [ - "Annotation", - "Standardisation and normalisation" - ], - "EDAM topic": [ - "Metabolomics", - "Compound libraries and screening", - "Data submission, annotation and curation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/MSMetaEnhancer", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer", - "Galaxy wrapper version": "0.4.0", - "Conda id": "msmetaenhancer", - "Conda version": "0.4.0", - "EDAM operation (no superclasses)": [ - "Annotation", - "Standardisation and normalisation" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics", - "Compound libraries and screening", - "Data submission, annotation and curation" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "msp_merge", - "Galaxy tool ids": [ - "msp_merge" - ], - "Description": null, - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge", - "Galaxy wrapper version": "0.1.0", - "Conda id": "matchms", - "Conda version": "0.26.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "mzml_validator", - "Galaxy tool ids": [ - "mzml_validator" - ], - "Description": "mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools", - "ToolShed categories": [ - "Metabolomics", - "Proteomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator", - "Galaxy wrapper version": "0.1.0+galaxy2", - "Conda id": "lxml", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "qcxms", - "Galaxy tool ids": [ - "qcxms_getres", - "qcxms_neutral_run", - "qcxms_production_run" - ], - "Description": "QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/grimme-lab/QCxMS", - "ToolShed categories": [ - "Computational chemistry", - "Molecular Dynamics" - ], - "ToolShed id": "QCxMS", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms", - "Galaxy wrapper version": "5.2.1", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 3, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "query", - "Galaxy tool ids": [ - "query" - ], - "Description": "Execute an SQL statement on a set of tables", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Text Manipulation" - ], - "ToolShed id": "query", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/query", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/query", - "Galaxy wrapper version": "0.2", - "Conda id": "click", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ramclustr", - "Galaxy tool ids": [ - "ramclustr", - "ramclustr_define_experiment" - ], - "Description": null, - "bio.tool id": "ramclustr", - "bio.tool ids": [ - "ramclustr" - ], - "biii": null, - "bio.tool name": "RAMClustR", - "bio.tool description": "A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.", - "EDAM operation": [ - "Imputation", - "Standardisation and normalisation", - "Clustering", - "Correlation" - ], - "EDAM topic": [ - "Metabolomics" - ], - "Status": "To update", - "Source": "https://rdrr.io/cran/RAMClustR/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr", - "Galaxy wrapper version": "1.3.0", - "Conda id": "r-ramclustr", - "Conda version": "1.3.1", - "EDAM operation (no superclasses)": [ - "Imputation", - "Standardisation and normalisation", - "Clustering", - "Correlation" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics" - ], - "Available on UseGalaxy.org": 2, - "Available on UseGalaxy.org.au": 2, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 2 - }, - { - "Galaxy wrapper id": "recetox_aplcms", - "Galaxy tool ids": [ - "recetox_aplcms_align_features", - "recetox_aplcms_compute_clusters", - "recetox_aplcms_compute_template", - "recetox_aplcms_correct_time", - "recetox_aplcms_generate_feature_table", - "recetox_aplcms_merge_known_table", - "recetox_aplcms_recover_weaker_signals", - "recetox_aplcms_remove_noise" - ], - "Description": "Peak detection tool for HRMS profile data.", - "bio.tool id": "recetox-aplcms", - "bio.tool ids": [ - "recetox-aplcms" - ], - "biii": null, - "bio.tool name": "recetox-aplcms", - "bio.tool description": "recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.", - "EDAM operation": [ - "Chromatographic alignment", - "Quantification", - "Peak detection", - "Feature extraction", - "Alignment" - ], - "EDAM topic": [ - "Metabolomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/recetox-aplcms", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "recetox-aplcms", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms", - "Galaxy wrapper version": "0.12.0", - "Conda id": "r-recetox-aplcms", - "Conda version": "0.12.0", - "EDAM operation (no superclasses)": [ - "Chromatographic alignment", - "Quantification", - "Peak detection", - "Feature extraction", - "Alignment" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 8, - "Available on UseGalaxy.eu": 8, - "Available on UseGalaxy.org.fr": 8 - }, - { - "Galaxy wrapper id": "recetox_msfinder", - "Galaxy tool ids": [ - "recetox_msfinder" - ], - "Description": null, - "bio.tool id": "recetox-msfinder", - "bio.tool ids": [ - "recetox-msfinder" - ], - "biii": null, - "bio.tool name": "recetox-msfinder", - "bio.tool description": "This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.", - "EDAM operation": [ - "Annotation" - ], - "EDAM topic": [ - "Metabolomics" - ], - "Status": "To update", - "Source": "https://github.com/RECETOX/recetox-msfinder", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder", - "Galaxy wrapper version": "v3.5.2", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Annotation" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "recetox_xmsannotator", - "Galaxy tool ids": [ - "recetox_xmsannotator_advanced" - ], - "Description": null, - "bio.tool id": "recetox-xmsannotator", - "bio.tool ids": [ - "recetox-xmsannotator" - ], - "biii": null, - "bio.tool name": "recetox-xMSannotator", - "bio.tool description": "Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.", - "EDAM operation": [ - "Expression profile pathway mapping", - "Structure comparison", - "Isotopic distributions calculation", - "Annotation" - ], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/recetox-xMSannotator", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator", - "Galaxy wrapper version": "0.10.0", - "Conda id": "r-recetox-xmsannotator", - "Conda version": "0.10.0", - "EDAM operation (no superclasses)": [ - "Expression profile pathway mapping", - "Structure comparison", - "Isotopic distributions calculation", - "Annotation" - ], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rem_complex", - "Galaxy tool ids": [ - "rem_complex" - ], - "Description": "Removes molecular coordination complexes.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "rem_complex", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex", - "Galaxy wrapper version": "1.0.0", - "Conda id": "pandas", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "rename_annotated_feature", - "Galaxy tool ids": [ - "rename_annotated_feature" - ], - "Description": "Update column names in an abundance table using a annotation table with spectral matching results", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/RECETOX/galaxytools/", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "rename_annotated_feature", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature", - "Galaxy wrapper version": "1.0.0", - "Conda id": "pandas", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "retip", - "Galaxy tool ids": [ - "retip_apply", - "retip_descriptors", - "retip_filter_rt", - "retip_train" - ], - "Description": null, - "bio.tool id": "retip", - "bio.tool ids": [ - "retip" - ], - "biii": null, - "bio.tool name": "Retip", - "bio.tool description": "Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.", - "EDAM operation": [ - "Retention time prediction", - "Spectrum calculation", - "Deisotoping", - "Formatting", - "Deposition" - ], - "EDAM topic": [ - "Metabolomics", - "Proteomics experiment", - "Machine learning", - "Cheminformatics", - "Chemistry" - ], - "Status": "To update", - "Source": "https://github.com/PaoloBnn/Retip", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/retip", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/retip", - "Galaxy wrapper version": "0.5.4", - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [ - "Retention time prediction", - "Spectrum calculation", - "Deisotoping", - "Formatting", - "Deposition" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics", - "Proteomics experiment", - "Machine learning", - "Cheminformatics", - "Chemistry" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "riassigner", - "Galaxy tool ids": [ - "riassigner", - "riassigner_from_comment" - ], - "Description": null, - "bio.tool id": "riassigner", - "bio.tool ids": [ - "riassigner" - ], - "biii": null, - "bio.tool name": "RIAssigner", - "bio.tool description": "RIAssigner is a python tool for retention index (RI) computation for GC-MS data.", - "EDAM operation": [ - "Standardisation and normalisation" - ], - "EDAM topic": [ - "Metabolomics", - "Compound libraries and screening", - "Data submission, annotation and curation" - ], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/RIAssigner", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner", - "Galaxy wrapper version": "0.4.1", - "Conda id": "riassigner", - "Conda version": "0.4.1", - "EDAM operation (no superclasses)": [ - "Standardisation and normalisation" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics", - "Compound libraries and screening", - "Data submission, annotation and curation" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 2, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "rmassbank", - "Galaxy tool ids": [ - "rmassbank" - ], - "Description": "RMassBank is an R package for processing tandem MS files and building of MassBank records.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/MassBank/RMassBank", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "rmassbank", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank", - "Galaxy wrapper version": "3.0.0", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 1, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "spec2vec", - "Galaxy tool ids": [ - "spec2vec_similarity", - "spec2vec_training" - ], - "Description": "Mass spectra similarity scoring using a trained Spec2Vec model.", - "bio.tool id": "spec2vec", - "bio.tool ids": [ - "spec2vec" - ], - "biii": null, - "bio.tool name": "Spec2Vec", - "bio.tool description": "Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.", - "EDAM operation": [ - "Spectrum calculation", - "Spectral library search", - "Database search", - "Natural product identification" - ], - "EDAM topic": [ - "Proteomics experiment", - "Metabolomics", - "Natural language processing", - "Proteomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/iomega/spec2vec", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "spec2vec", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec", - "Galaxy wrapper version": "0.8.0", - "Conda id": "spec2vec", - "Conda version": "0.8.0", - "EDAM operation (no superclasses)": [ - "Spectrum calculation", - "Spectral library search", - "Database search", - "Natural product identification" - ], - "EDAM topic (no superclasses)": [ - "Proteomics experiment", - "Metabolomics", - "Natural language processing", - "Proteomics" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "waveica", - "Galaxy tool ids": [ - "waveica" - ], - "Description": "Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.", - "bio.tool id": "waveica", - "bio.tool ids": [ - "waveica" - ], - "biii": null, - "bio.tool name": "WaveICA", - "bio.tool description": "Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.", - "EDAM operation": [ - "Standardisation and normalisation" - ], - "EDAM topic": [ - "Metabolomics" - ], - "Status": "Up-to-date", - "Source": "https://github.com/RECETOX/WaveICA", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": null, - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/waveica", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/waveica", - "Galaxy wrapper version": "0.2.0", - "Conda id": "r-recetox-waveica", - "Conda version": "0.2.0", - "EDAM operation (no superclasses)": [ - "Standardisation and normalisation" - ], - "EDAM topic (no superclasses)": [ - "Metabolomics" - ], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "xtb", - "Galaxy tool ids": [ - "xtb_molecular_optimization" - ], - "Description": "Performs semiempirical molecular optimization.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/grimme-lab/xtb", - "ToolShed categories": [ - "Metabolomics" - ], - "ToolShed id": "xtb_molecular_optimization", - "Galaxy wrapper owner": "recetox", - "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/xtb", - "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/xtb", - "Galaxy wrapper version": "6.6.1", - "Conda id": "xtb", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 1 - }, - { - "Galaxy wrapper id": "consolidate_vcfs", - "Galaxy tool ids": [ - "consolidate_vcfs" - ], - "Description": "Combines freebayes and mpileup files for use by vcf2snvalignment", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "consolidate_vcfs", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_density", - "Galaxy tool ids": [ - "filterdensity" - ], - "Description": "Filter out position based on distance between SNVs", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "filter_density", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_stats", - "Galaxy tool ids": [ - "filterstat" - ], - "Description": "SNVPhyl filter_stats", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "filter_stats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "filter_vcf", - "Galaxy tool ids": [ - "filtervcf" - ], - "Description": "SNVPhyl filter_vcf", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "filter_vcf", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "find_repeats", - "Galaxy tool ids": [ - "findrepeat" - ], - "Description": "Find repetitive regions on a reference genome using MUMMer", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "find_repeats", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "positions2snv_alignment", - "Galaxy tool ids": [ - "positions2snv_alignment" - ], - "Description": "Generate alignment of SNVs from SNVPhyl variant table.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "positions2snv_alignment", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "positions2snv_invariant_alignment", - "Galaxy tool ids": [ - "positions2snv_invariant_alignment" - ], - "Description": "Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Variant Analysis" - ], - "ToolShed id": "positions2snv_invariant_alignment", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "snv_matrix", - "Galaxy tool ids": [ - "snvmatrix" - ], - "Description": "Generate matrix of SNV distances", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "snv_matrix", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "vcf2snvalignment", - "Galaxy tool ids": [ - "vcf2snvalignment" - ], - "Description": "Generates multiple alignment of variant calls", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "vcf2snvalignment", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "verify_map", - "Galaxy tool ids": [ - "verify_map" - ], - "Description": "Checks the mapping quality of all BAM(s)", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "Up-to-date", - "Source": "https://snvphyl.readthedocs.io/en/latest/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "verify_map", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map", - "Galaxy wrapper version": "1.8.2", - "Conda id": "snvphyl-tools", - "Conda version": "1.8.2", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "suite_snvphyl", - "Galaxy tool ids": [], - "Description": "SNVPhyl suite defining all dependencies for SNVPhyl", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "suite_snvphyl_1_2_3", - "Galaxy wrapper owner": "nml", - "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", - "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl", - "Galaxy wrapper version": null, - "Conda id": null, - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "cooler", - "Galaxy tool ids": [ - "cooler_balance", - "cooler_cload_tabix", - "cooler_csort_tabix", - "cooler_makebins", - "cooler_zoomify" - ], - "Description": "cooler different tools to process Hi-C from mirnylab", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/open2c/cooler", - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "cooler", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler", - "Galaxy wrapper version": "0.9.3", - "Conda id": "htslib", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 4, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 5, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fromHicupToJuicebox", - "Galaxy tool ids": [ - "fromHicupToJuicebox" - ], - "Description": "Convert the output of hicup (as sam or bam) to the input of juicebox.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "from_hicup_to_juicebox", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox", - "Galaxy wrapper version": "0.0.2", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "fromgtfTobed12", - "Galaxy tool ids": [ - "fromgtfTobed12" - ], - "Description": "Convert GTF files to BED12 format", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://pythonhosted.org/gffutils/contents.html", - "ToolShed categories": [ - "Convert Formats" - ], - "ToolShed id": "fromgtftobed12", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12", - "Galaxy wrapper version": "0.11.1+galaxy1", - "Conda id": "gffutils", - "Conda version": "0.13", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "getTn5ExtendedCoverage", - "Galaxy tool ids": [ - "getTn5ExtendedCoverage" - ], - "Description": "Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Epigenetics" - ], - "ToolShed id": "gettn5extendedcoverage", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": null, - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage", - "Galaxy wrapper version": "0.0.2", - "Conda id": "pysam", - "Conda version": "0.22.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "hyperstack_to_bleach_corrected_movie", - "Galaxy tool ids": [ - "hyperstack_to_bleach_corrected_movie" - ], - "Description": "Generate blach corrected movie from hyperstack", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "hyperstack_to_bleach_corrected_movie", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie", - "Galaxy wrapper version": "20230328", - "Conda id": "Fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "incucyte_stack_and_upload_omero", - "Galaxy tool ids": [ - "incucyte_stack_and_upload_omero" - ], - "Description": "Combine images to stack and upload to the omero server", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "incucyte_stack_and_upload_omero", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero", - "Galaxy wrapper version": "20231221", - "Conda id": "Fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "measure_gastruloids", - "Galaxy tool ids": [ - "measureGastruloids" - ], - "Description": "Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "measure_gastruloids", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids", - "Galaxy wrapper version": "20221216", - "Conda id": "fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "omero_clean_rois_tables", - "Galaxy tool ids": [ - "omero_clean_rois_tables" - ], - "Description": "Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "omero_clean_rois_tables", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables", - "Galaxy wrapper version": "20230623", - "Conda id": "fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "omero_get_children_ids", - "Galaxy tool ids": [ - "omero_get_children_ids" - ], - "Description": "Get omero id of children of an omero object id", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "omero_get_children_ids", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids", - "Galaxy wrapper version": "0.1.0", - "Conda id": "omero-py", - "Conda version": "5.11.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "omero_get_full_images", - "Galaxy tool ids": [ - "omero_get_full_images" - ], - "Description": "Get full images from omero", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "omero_get_full_images", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images", - "Galaxy wrapper version": "20240521", - "Conda id": "fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "omero_hyperstack_to_fluo_measurements_on_gastruloid", - "Galaxy tool ids": [ - "omero_hyperstack_to_fluo_measurements_on_gastruloid" - ], - "Description": "Analyse Hyperstack on OMERO server to measure fluorescence levels", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "omero_hyperstack_to_fluo_measurements_on_gastruloid", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid", - "Galaxy wrapper version": "20230809", - "Conda id": "fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "omero_hyperstack_to_gastruloid_measurements", - "Galaxy tool ids": [ - "omero_hyperstack_to_gastruloid_measurements" - ], - "Description": "Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "omero_hyperstack_to_gastruloid_measurements", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements", - "Galaxy wrapper version": "20240214", - "Conda id": "fiji", - "Conda version": "20231211", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "revertR2orientationInBam", - "Galaxy tool ids": [ - "revertR2orientationInBam" - ], - "Description": "Revert the mapped orientation of R2 mates in a bam.", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "SAM" - ], - "ToolShed id": "revertr2orientationinbam", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam", - "Galaxy wrapper version": "0.0.2", - "Conda id": "samtools", - "Conda version": "1.20", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 1, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "upload_roi_and_measures_to_omero", - "Galaxy tool ids": [ - "uploadROIandMeasuresToOMERO" - ], - "Description": "Upload the ROI coordinates and the measurements to the omero server", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": null, - "ToolShed categories": [ - "Imaging" - ], - "ToolShed id": "upload_roi_and_measures_to_omero", - "Galaxy wrapper owner": "lldelisle", - "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero", - "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero", - "Galaxy wrapper version": "0.0.5", - "Conda id": "omero-py", - "Conda version": "5.11.1", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast2go", - "Galaxy tool ids": [ - "blast2go" - ], - "Description": "Maps BLAST results to GO annotation terms", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", - "ToolShed categories": [ - "Ontology Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "blast2go", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", - "Galaxy wrapper version": "0.0.11", - "Conda id": "b2g4pipe", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blast_rbh", - "Galaxy tool ids": [ - "blast_reciprocal_best_hits" - ], - "Description": "BLAST Reciprocal Best Hits (RBH) from two FASTA files", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "blast_rbh", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", - "Galaxy wrapper version": "0.3.0", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "blastxml_to_top_descr", - "Galaxy tool ids": [ - "blastxml_to_top_descr" - ], - "Description": "Make table of top BLAST match descriptions", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", - "ToolShed categories": [ - "Convert Formats", - "Sequence Analysis", - "Text Manipulation" - ], - "ToolShed id": "blastxml_to_top_descr", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", - "Galaxy wrapper version": "0.1.2", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 1, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "make_nr", - "Galaxy tool ids": [ - "make_nr" - ], - "Description": "Make a FASTA file non-redundant", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", - "ToolShed categories": [ - "Fasta Manipulation", - "Sequence Analysis" - ], - "ToolShed id": "make_nr", - "Galaxy wrapper owner": "peterjc", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", - "Galaxy wrapper version": "0.0.2", - "Conda id": "biopython", - "Conda version": "1.70", - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 0 - }, - { - "Galaxy wrapper id": "ncbi_blast_plus", - "Galaxy tool ids": [ - "blastxml_to_tabular", - "get_species_taxids", - "ncbi_blastdbcmd_info", - "ncbi_blastdbcmd_wrapper", - "ncbi_blastn_wrapper", - "ncbi_blastp_wrapper", - "ncbi_blastx_wrapper", - "ncbi_convert2blastmask_wrapper", - "ncbi_deltablast_wrapper", - "ncbi_dustmasker_wrapper", - "ncbi_makeblastdb", - "ncbi_makeprofiledb", - "ncbi_psiblast_wrapper", - "ncbi_rpsblast_wrapper", - "ncbi_rpstblastn_wrapper", - "ncbi_segmasker_wrapper", - "ncbi_tblastn_wrapper", - "ncbi_tblastx_wrapper" - ], - "Description": "NCBI BLAST+", - "bio.tool id": null, - "bio.tool ids": [], - "biii": null, - "bio.tool name": null, - "bio.tool description": null, - "EDAM operation": [], - "EDAM topic": [], - "Status": "To update", - "Source": "https://blast.ncbi.nlm.nih.gov/", - "ToolShed categories": [ - "Sequence Analysis" - ], - "ToolShed id": "ncbi_blast_plus", - "Galaxy wrapper owner": "devteam", - "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", - "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", - "Galaxy wrapper version": "2.14.1", - "Conda id": "python", - "Conda version": null, - "EDAM operation (no superclasses)": [], - "EDAM topic (no superclasses)": [], - "Available on UseGalaxy.org": 16, - "Available on UseGalaxy.org.au": 16, - "Available on UseGalaxy.eu": 16, - "Available on UseGalaxy.org.fr": 16 - }, - { - "Galaxy wrapper id": "frogs", - "Galaxy tool ids": [ - "FROGS_affiliation_filters", - "FROGS_affiliation_postprocess", - "FROGS_affiliation_stats", - "FROGS_biom_to_stdBiom", - "FROGS_biom_to_tsv", - "FROGS_cluster_filters", - "FROGS_cluster_stats", - "FROGS_clustering", - "FROGS_demultiplex", - "FROGSSTAT_DESeq2_Preprocess", - "FROGSSTAT_DESeq2_Visualisation", - "FROGSFUNC_step2_functions", - "FROGSFUNC_step3_pathways", - "FROGSFUNC_step1_placeseqs", - "FROGS_itsx", - "FROGS_normalisation", - "FROGSSTAT_Phyloseq_Alpha_Diversity", - "FROGSSTAT_Phyloseq_Beta_Diversity", - "FROGSSTAT_Phyloseq_Sample_Clustering", - "FROGSSTAT_Phyloseq_Composition_Visualisation", - "FROGSSTAT_Phyloseq_Import_Data", - "FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance", - "FROGSSTAT_Phyloseq_Structure_Visualisation", - "FROGS_preprocess", - "FROGS_remove_chimera", - "FROGS_taxonomic_affiliation", - "FROGS_Tree", - "FROGS_tsv_to_biom" - ], - "Description": "Suite for metabarcoding analysis", - "bio.tool id": "frogs", - "bio.tool ids": [ - "frogs" - ], - "biii": null, - "bio.tool name": "FROGS", - "bio.tool description": "The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.", - "EDAM operation": [ - "Taxonomic classification" - ], - "EDAM topic": [ - "Metagenomics", - "Microbial ecology", - "Taxonomy", - "Evolutionary biology", - "Sequencing" - ], - "Status": "Up-to-date", - "Source": "http://frogs.toulouse.inrae.fr/", - "ToolShed categories": [ - "Metagenomics" - ], - "ToolShed id": "frogs", - "Galaxy wrapper owner": "frogs", - "Galaxy wrapper source": "https://github.com/geraldinepascal/FROGS-wrappers/", - "Galaxy wrapper parsed folder": "https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs", - "Galaxy wrapper version": "4.1.0", - "Conda id": "frogs", - "Conda version": "4.1.0", - "EDAM operation (no superclasses)": [ - "Taxonomic classification" - ], - "EDAM topic (no superclasses)": [ - "Metagenomics", - "Microbial ecology", - "Taxonomy", - "Evolutionary biology", - "Sequencing" - ], - "Available on UseGalaxy.org": 0, - "Available on UseGalaxy.org.au": 0, - "Available on UseGalaxy.eu": 0, - "Available on UseGalaxy.org.fr": 28 - } - ] + { + "Galaxy wrapper id": "askor", + "Galaxy tool ids": [ + "askor_de" + ], + "Description": "AskoR links EdgeR and AskOmics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/askomics/askoR", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "askor_de", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/askor", + "Galaxy wrapper version": "0.2", + "Conda id": "bioconductor-limma", + "Conda version": "3.58.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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", + "Galaxy tool ids": [ + "baric_archive_rennes", + "baric_archive_toulouse" + ], + "Description": "A data source tool to fetch data from a BARIC Archive server.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.cesgo.org/catibaric/", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive", + "Galaxy wrapper version": "1.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "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", + "Galaxy tool ids": [ + "braker" + ], + "Description": "BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Gaius-Augustus/BRAKER", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "braker", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", + "Galaxy wrapper version": "2.1.6", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "braker3", + "Galaxy tool ids": [ + "braker3" + ], + "Description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .", + "bio.tool id": "braker3", + "bio.tool ids": [ + "braker3" + ], + "biii": null, + "bio.tool name": "BRAKER3", + "bio.tool description": "BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes", + "EDAM operation": [ + "Genome annotation", + "Gene prediction" + ], + "EDAM topic": [ + "RNA-Seq", + "Genomics", + "Structure prediction", + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/Gaius-Augustus/BRAKER", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "braker3", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/braker3", + "Galaxy wrapper version": "3.0.8", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Genome annotation", + "Gene prediction" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Genomics", + "Structure prediction", + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "feelnc2asko", + "Galaxy tool ids": [ + "feelnc2asko" + ], + "Description": "Convert FeelNC GTF to GFF3", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/tderrien/FEELnc", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "feelnc2asko", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko", + "Galaxy wrapper version": "0.1", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "gcms2isocor", + "Galaxy tool ids": [ + "gcms2isocor" + ], + "Description": "Conversion from GCMS PostRun Analysis to Isocor", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "gcms2isocor", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor", + "Galaxy wrapper version": "0.1.0", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "get_pairs", + "Galaxy tool ids": [ + "get_pairs" + ], + "Description": "Separate paired and unpaired reads from two fastq files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "get_pairs", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs", + "Galaxy wrapper version": "0.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "helixer", + "Galaxy tool ids": [ + "helixer" + ], + "Description": "Gene calling with Deep Neural Networks", + "bio.tool id": "helixer", + "bio.tool ids": [ + "helixer" + ], + "biii": null, + "bio.tool name": "Helixer", + "bio.tool description": "Deep Learning to predict gene annotations", + "EDAM operation": [ + "Gene prediction", + "Genome annotation" + ], + "EDAM topic": [ + "Sequence analysis", + "Gene transcripts" + ], + "Status": "To update", + "Source": "https://github.com/weberlab-hhu/Helixer", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "helixer", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/helixer", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/helixer", + "Galaxy wrapper version": "0.3.3", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Gene prediction", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Gene transcripts" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "logol", + "Galaxy tool ids": [ + "logol_wrapper" + ], + "Description": "Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://logol.genouest.org/web/app.php/logol", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/logol", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/logol", + "Galaxy wrapper version": "1.7.8", + "Conda id": "logol", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "meneco", + "Galaxy tool ids": [ + "meneco" + ], + "Description": "Meneco computes minimal completions to your draft network with reactions from a repair network", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://bioasp.github.io/meneco/", + "ToolShed categories": [ + "Systems Biology" + ], + "ToolShed id": "meneco", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/meneco", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/meneco", + "Galaxy wrapper version": "1.5.2", + "Conda id": "meneco", + "Conda version": "1.5.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "miranda2asko", + "Galaxy tool ids": [ + "miranda2asko" + ], + "Description": "Converts miRanda output into AskOmics format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "miranda2asko", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": "https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko", + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko", + "Galaxy wrapper version": "0.2", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "openlabcds2csv", + "Galaxy tool ids": [ + "openlabcds2csv" + ], + "Description": "Creates a summary of several \"Internal Standard Report\" OpenLabCDS results.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "openlabcds2csv", + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv", + "Galaxy wrapper version": "0.1.0", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "peptimapper", + "Galaxy tool ids": [ + "peptimapper_clustqualify", + "peptimapper_clust_to_gff", + "peptimapper_pep_match", + "peptimapper_pep_novo_tag" + ], + "Description": "Proteogenomics workflow for the expert annotation of eukaryotic genomes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "genouest", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper", + "Galaxy wrapper version": "2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "Ensembl-REST", + "Galaxy tool ids": [ + "get_feature_info", + "get_genetree", + "get_sequences" + ], + "Description": "A suite of Galaxy tools designed to work with Ensembl REST API.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://rest.ensembl.org", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST", + "Galaxy wrapper version": "0.1.2", + "Conda id": "requests", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 3, + "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": 3, + "Tools available on UseGalaxy.no": 3 + }, + { + "Galaxy wrapper id": "GAFA", + "Galaxy tool ids": [ + "gafa" + ], + "Description": "Gene Align and Family Aggregator", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://aequatus.tgac.ac.uk", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "gafa", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA", + "Galaxy wrapper version": "0.3.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "TreeBest", + "Galaxy tool ids": [ + "treebest_best" + ], + "Description": "TreeBeST best", + "bio.tool id": "treebest", + "bio.tool ids": [ + "treebest" + ], + "biii": null, + "bio.tool name": "TreeBeST", + "bio.tool description": "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.", + "EDAM operation": [ + "Phylogenetic tree visualisation", + "Phylogenetic analysis", + "Phylogenetic inference (from molecular sequences)" + ], + "EDAM topic": [ + "Phylogenetics" + ], + "Status": "To update", + "Source": "http://treesoft.sourceforge.net/treebest.shtml", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "treebest_best", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest", + "Galaxy wrapper version": "1.9.2.post0", + "Conda id": "treebest", + "Conda version": "1.9.2.post1", + "EDAM operation (no superclasses)": [ + "Phylogenetic tree visualisation", + "Phylogenetic inference (from molecular sequences)" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "apoc", + "Galaxy tool ids": [ + "apoc" + ], + "Description": "Large-scale structural comparison of protein pockets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://cssb.biology.gatech.edu/APoc", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "apoc", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc", + "Galaxy wrapper version": "1.0+galaxy1", + "Conda id": "apoc", + "Conda version": "1b16", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "blast_parser", + "Galaxy tool ids": [ + "blast_parser" + ], + "Description": "Convert 12- or 24-column BLAST output into 3-column hcluster_sg input", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/TGAC/earlham-galaxytools/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "blast_parser", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser", + "Galaxy wrapper version": "0.1.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 0, + "Tools available on ANASTASIA": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "ete", + "Galaxy tool ids": [ + "ete_gene_csv_finder", + "ete_genetree_splitter", + "ete_homology_classifier", + "ete_init_taxdb", + "ete_lineage_generator", + "ete3_mod", + "ete_species_tree_generator" + ], + "Description": "Analyse phylogenetic trees using the ETE Toolkit", + "bio.tool id": "ete", + "bio.tool ids": [ + "ete" + ], + "biii": null, + "bio.tool name": "ete", + "bio.tool description": "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", + "EDAM operation": [ + "Phylogenetic analysis", + "Phylogenetic tree editing" + ], + "EDAM topic": [ + "Phylogenetics" + ], + "Status": "To update", + "Source": "http://etetoolkit.org/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "ete", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete", + "Galaxy wrapper version": "3.1.2", + "Conda id": "ete3", + "Conda version": "3.1.1", + "EDAM operation (no superclasses)": [ + "Phylogenetic tree editing" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.fr": 7, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 7, + "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": 7, + "Tools available on UseGalaxy.no": 7 + }, + { + "Galaxy wrapper id": "export_to_cluster", + "Galaxy tool ids": [ + "export_to_cluster" + ], + "Description": "Export datasets to cluster", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/TGAC/earlham-galaxytools/", + "ToolShed categories": [ + "Data Export" + ], + "ToolShed id": "export_to_cluster", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster", + "Galaxy wrapper version": "0.0.2", + "Conda id": "EXPORT_DIR_PREFIX", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "gblocks", + "Galaxy tool ids": [ + "gblocks" + ], + "Description": "Gblocks", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://molevol.cmima.csic.es/castresana/Gblocks.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gblocks", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks", + "Galaxy wrapper version": "0.91b", + "Conda id": "gblocks", + "Conda version": "0.91b", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "gstf_preparation", + "Galaxy tool ids": [ + "gstf_preparation" + ], + "Description": "GeneSeqToFamily preparation converts data for the workflow", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/TGAC/earlham-galaxytools/", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "gstf_preparation", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation", + "Galaxy wrapper version": "0.4.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "hcluster_sg", + "Galaxy tool ids": [ + "hcluster_sg" + ], + "Description": "Hierarchically clustering on a sparse graph", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/douglasgscofield/hcluster", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "hcluster_sg", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg", + "Galaxy wrapper version": "0.5.1.1", + "Conda id": "hcluster_sg", + "Conda version": "0.5.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "hcluster_sg_parser", + "Galaxy tool ids": [ + "hcluster_sg_parser" + ], + "Description": "Converts hcluster_sg 3-column output into lists of ids", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/TGAC/earlham-galaxytools/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "hcluster_sg_parser", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser", + "Galaxy wrapper version": "0.2.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "lotus2", + "Galaxy tool ids": [ + "lotus2" + ], + "Description": "LotuS2 OTU processing pipeline", + "bio.tool id": "lotus2", + "bio.tool ids": [ + "lotus2" + ], + "biii": null, + "bio.tool name": "lotus2", + "bio.tool description": "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.", + "EDAM operation": [ + "Sequence feature detection", + "DNA barcoding" + ], + "EDAM topic": [ + "Metagenomics", + "Taxonomy", + "Microbial ecology" + ], + "Status": "Up-to-date", + "Source": "http://lotus2.earlham.ac.uk/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "lotus2", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2", + "Galaxy wrapper version": "2.32", + "Conda id": "lotus2", + "Conda version": "2.32", + "EDAM operation (no superclasses)": [ + "Sequence feature detection", + "DNA barcoding" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Taxonomy", + "Microbial ecology" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "miranda", + "Galaxy tool ids": [ + "miranda" + ], + "Description": "Finds potential target sites for miRNAs in genomic sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.microrna.org/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "miranda", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda", + "Galaxy wrapper version": "3.3a+galaxy1", + "Conda id": "miranda", + "Conda version": "3.3a", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": "plotheatmap", + "Galaxy tool ids": [ + "plotheatmap" + ], + "Description": "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.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "plotheatmap", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap", + "Galaxy wrapper version": "1.0", + "Conda id": "bioconductor-preprocesscore", + "Conda version": "1.64.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "rdock", + "Galaxy tool ids": [ + "rdock" + ], + "Description": "Docking ligands to proteins and nucleic acids", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rdock.sourceforge.net/", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "rdock", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock", + "Galaxy wrapper version": "1.0", + "Conda id": "rDock", + "Conda version": "2013.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "replace_chromosome_names", + "Galaxy tool ids": [ + "replace_chromosome_names" + ], + "Description": "Replace chromosome names", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "replace_chromosome_names", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names", + "Galaxy wrapper version": "0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rsat_filter_snps", + "Galaxy tool ids": [ + "rsat_filter_snps" + ], + "Description": "Filter SNPs in RSAT Matrix Scan output", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/TGAC/earlham-galaxytools/", + "ToolShed categories": [ + "ChIP-seq", + "Systems Biology" + ], + "ToolShed id": "rsat_filter_snps", + "Galaxy wrapper owner": "earlham", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "smart_domains", + "Galaxy tool ids": [ + "smart_domains" + ], + "Description": "SMART domains", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://smart.embl.de/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "smart_domains", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains", + "Galaxy wrapper version": "0.1.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "smina", + "Galaxy tool ids": [ + "smina" + ], + "Description": "smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://sourceforge.net/projects/smina/", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "smina", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina", + "Galaxy wrapper version": "1.0", + "Conda id": "smina", + "Conda version": "2017.11.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "t_coffee", + "Galaxy tool ids": [ + "t_coffee" + ], + "Description": "T-Coffee", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.tcoffee.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "t_coffee", + "Galaxy wrapper owner": "earlhaminst", + "Galaxy wrapper source": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee", + "Galaxy wrapper parsed folder": "https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee", + "Galaxy wrapper version": "13.45.0.4846264", + "Conda id": "t-coffee", + "Conda version": "13.46.0.919e8c6b", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "abacas", + "Galaxy tool ids": [ + "abacas" + ], + "Description": "Order and Orientate Contigs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/abacas", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "abacas", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/abacas", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas", + "Galaxy wrapper version": "1.1", + "Conda id": "mummer", + "Conda version": "3.23", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": "assemblystats", + "Galaxy tool ids": [ + "assemblystats" + ], + "Description": "Summarise an assembly (e.g. N50 metrics)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "assemblystats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats", + "Galaxy wrapper version": "1.1.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "bam2mappingstats", + "Galaxy tool ids": [ + "bam2mappingstats" + ], + "Description": "Generates mapping stats from a bam file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "bam2mappingstats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats", + "Galaxy wrapper version": "1.1.0", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "bamclipper", + "Galaxy tool ids": [ + "bamclipper" + ], + "Description": "Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/tommyau/bamclipper", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bamclipper", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/tommyau/bamclipper", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bamclipper", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "biohansel", + "Galaxy tool ids": [ + "biohansel" + ], + "Description": "Heidelberg and Enteritidis SNP Elucidation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/biohansel", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "biohansel", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/biohansel", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel", + "Galaxy wrapper version": "2.4.0", + "Conda id": "bio_hansel", + "Conda version": "2.6.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "biohansel_bionumeric_converter", + "Galaxy tool ids": [ + "bionumeric_convert" + ], + "Description": "Convert BioHansel output data to a Bionumerics friendly form", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "biohansel_bionumeric_converter", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter", + "Galaxy wrapper version": "0.2.0", + "Conda id": "pandas", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "bundle_collections", + "Galaxy tool ids": [ + "bundle_collection" + ], + "Description": "Tool to bundle up list collection into a single zip to be download", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bundle_collections", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections", + "Galaxy wrapper version": "1.3.0", + "Conda id": "perl-getopt-long", + "Conda version": "2.54", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": "collapse_collection", + "Galaxy tool ids": [ + "collapse_dataset" + ], + "Description": "Collection tool that collapses a list of files into a single datasset in order of appears in collection", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "collapse_collections", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection", + "Galaxy wrapper version": "5.1.0", + "Conda id": "gawk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "combineJSON", + "Galaxy tool ids": [ + "combine_json" + ], + "Description": "JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "combine_json", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "combine_assembly_stats", + "Galaxy tool ids": [ + "combine_stats" + ], + "Description": "Combine multiple Assemblystats datasets into a single tabular report", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "combine_assemblystats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats", + "Galaxy wrapper version": "1.0", + "Conda id": "perl-getopt-long", + "Conda version": "2.54", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "combine_tabular_collection", + "Galaxy tool ids": [ + "combine" + ], + "Description": "Combine Tabular Collection into a single file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "combine_tabular_collection", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "concat_paired", + "Galaxy tool ids": [ + "concat_fastqs" + ], + "Description": "Concatenate paired datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/concat", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "concat_paired", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/concat", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired", + "Galaxy wrapper version": "0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "cryptogenotyper", + "Galaxy tool ids": [ + "CryptoGenotyper" + ], + "Description": "CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/CryptoGenotyper", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "cryptogenotyper", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/CryptoGenotyper", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper", + "Galaxy wrapper version": "1.0", + "Conda id": "cryptogenotyper", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "csvtk", + "Galaxy tool ids": [ + "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" + ], + "Description": "Rapid data investigation and manipulation of csv/tsv files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioinf.shenwei.me/csvtk/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "csvtk", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/shenwei356/csvtk", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk", + "Galaxy wrapper version": "0.20.0", + "Conda id": "csvtk", + "Conda version": "0.30.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": 20, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": "ectyper", + "Galaxy tool ids": [ + "ectyper" + ], + "Description": "EC-Typer - in silico serotyping of Escherichia coli species", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/ecoli_serotyping", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ectyper", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/ecoli_serotyping", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper", + "Galaxy wrapper version": "1.0.0", + "Conda id": "ectyper", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "fasta2bed", + "Galaxy tool ids": [ + "fasta2bed" + ], + "Description": "Convert multiple fasta file into tabular bed file format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fasta2bed", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed", + "Galaxy wrapper version": "1.0.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "fasta_extract", + "Galaxy tool ids": [ + "fa-extract-sequence" + ], + "Description": "extract single fasta from multiple fasta file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fasta_extract", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract", + "Galaxy wrapper version": "1.1.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "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": "fastqc_stats", + "Galaxy tool ids": [ + "FastQC_Summary" + ], + "Description": "Summary multiple FastQC into a single tabular line report", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fastqc_stats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats", + "Galaxy wrapper version": "1.2", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "feht", + "Galaxy tool ids": [ + "feht" + ], + "Description": "Automatically identify makers predictive of groups.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "feht", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht", + "Galaxy wrapper version": "0.1.0", + "Conda id": "feht", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "filter_spades_repeats", + "Galaxy tool ids": [ + "filter_spades_repeat" + ], + "Description": "Remove short and repeat contigs/scaffolds", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "filter_spades_repeats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats", + "Galaxy wrapper version": "1.0.1", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "getmlst", + "Galaxy tool ids": [ + "getmlst" + ], + "Description": "Download MLST datasets by species from pubmlst.org", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "getmlst", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst", + "Galaxy wrapper version": "0.1.4.1", + "Conda id": "srst2", + "Conda version": "0.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "gnali", + "Galaxy tool ids": [ + "gnali" + ], + "Description": "A tool to find nonessential, loss-of-function gene variants", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/gnali/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "gnali", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/gnali/", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali", + "Galaxy wrapper version": "1.1.0", + "Conda id": "gnali", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "hivtrace", + "Galaxy tool ids": [ + "hivtrace" + ], + "Description": "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.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "hivtrace", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace", + "Galaxy wrapper version": "1.0.1", + "Conda id": "hivtrace", + "Conda version": "1.5.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "kaptive", + "Galaxy tool ids": [ + "kaptive" + ], + "Description": "Kaptive reports information about capsular (K) loci found in genome assemblies.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "kaptive", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive", + "Galaxy wrapper version": "0.3.0", + "Conda id": "kaptive", + "Conda version": "3.0.0b1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "kat_filter", + "Galaxy tool ids": [ + "kat_@EXECUTABLE@" + ], + "Description": "Filtering kmers or reads from a database of kmers hashes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "kat_filter", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter", + "Galaxy wrapper version": "2.3", + "Conda id": "kat", + "Conda version": "2.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "kat_sect", + "Galaxy tool ids": [ + "kat_@EXECUTABLE@" + ], + "Description": "SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "kat_sect", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect", + "Galaxy wrapper version": "2.3", + "Conda id": "kat", + "Conda version": "2.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "mauve_contig_mover", + "Galaxy tool ids": [ + "mauve_contig_mover" + ], + "Description": "Order a draft genome relative to a related reference genome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/mauve_contig_mover", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mauve_contig_mover", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/mauve_contig_mover", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover", + "Galaxy wrapper version": "1.0.10", + "Conda id": "mauve", + "Conda version": "2.4.0.r4736", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "mob_suite", + "Galaxy tool ids": [ + "mob_recon", + "mob_typer" + ], + "Description": "MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/mob-suite", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mob_suite", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/mob-suite", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite", + "Galaxy wrapper version": "3.0.3", + "Conda id": "mob_suite", + "Conda version": "3.1.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 2, + "Tools available on UseGalaxy.org (Main)": 0, + "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": 2, + "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": "mrbayes", + "Galaxy tool ids": [ + "mrbayes" + ], + "Description": "A program for the Bayesian estimation of phylogeny.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mrbayes", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes", + "Galaxy wrapper version": "1.0.2", + "Conda id": "mrbayes", + "Conda version": "3.2.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 0, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "mykrobe_parser", + "Galaxy tool ids": [ + "mykrobe_parseR" + ], + "Description": "RScript to parse the results of mykrobe predictor.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/mykrobe-parser", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mykrobe_parser", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/mykrobe-parser", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser", + "Galaxy wrapper version": "0.1.4.1", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pangolin", + "Galaxy tool ids": [ + "pangolin" + ], + "Description": "Phylogenetic Assignment of Named Global Outbreak LINeages", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/hCoV-2019/pangolin", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pangolin", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/hCoV-2019/pangolin", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin", + "Galaxy wrapper version": "1.1.14", + "Conda id": "pangolin", + "Conda version": "4.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "patrist", + "Galaxy tool ids": [ + "patrist" + ], + "Description": "Extract Patristic Distance From a Tree", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "patrist", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/patrist", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist", + "Galaxy wrapper version": "0.1.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "plasmid_profiler", + "Galaxy tool ids": [ + "plasmid_profiler" + ], + "Description": "Explores plasmid content in WGS data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "plasmid_profiler", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler", + "Galaxy wrapper version": "0.1.6", + "Conda id": "r", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "plasmid_profiler_suite", + "Galaxy tool ids": [], + "Description": "Plasmid Profiler suite defining all dependencies for Plasmid Profiler", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "suite_plasmid_profiler", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "plasmidspades", + "Galaxy tool ids": [ + "plasmidspades" + ], + "Description": "Genome assembler for assemblying plasmid", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "plasmidspades", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades", + "Galaxy wrapper version": "1.1", + "Conda id": "spades", + "Conda version": "4.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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)": 1, + "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": 1, + "Tools available on GalaxyTrakr": 1, + "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": "pneumocat", + "Galaxy tool ids": [ + "pneumocat" + ], + "Description": "Pneumococcal Capsular Typing of illumina fastq reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phe-bioinformatics/PneumoCaT", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pneumocat", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phe-bioinformatics/PneumoCaT", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat", + "Galaxy wrapper version": "1.2.1", + "Conda id": "pneumocat", + "Conda version": "1.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "promer", + "Galaxy tool ids": [ + "promer4_substitutions" + ], + "Description": "Aligns two sets of contigs and reports amino acid substitutions between them", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/promer", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "promer", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/promer", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer", + "Galaxy wrapper version": "1.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pseudogenome", + "Galaxy tool ids": [ + "pseudogenome" + ], + "Description": "Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pseudogenome", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome", + "Galaxy wrapper version": "1.0.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "quasitools", + "Galaxy tool ids": [ + "aacoverage", + "aavariants", + "callcodonvar", + "callntvar", + "complexity_bam", + "complexity_fasta", + "consensus", + "distance", + "dnds", + "drmutations", + "hydra", + "quality" + ], + "Description": "A collection of tools for analysing Viral Quasispecies", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/quasitools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "quasitools", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/quasitools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools", + "Galaxy wrapper version": "0.7.0", + "Conda id": "quasitools", + "Conda version": "0.7.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 12, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 12, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 12, + "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": 12, + "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": "refseq_masher", + "Galaxy tool ids": [ + "refseq_masher_contains", + "refseq_masher_matches" + ], + "Description": "Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/refseq_masher", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "refseq_masher", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/refseq_masher", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher", + "Galaxy wrapper version": "0.1.2", + "Conda id": "refseq_masher", + "Conda version": "0.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 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": 2, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 2, + "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": "seqtk_nml", + "Galaxy tool ids": [ + "seqtk_nml_sample" + ], + "Description": "Tool to downsample fastq reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/lh3/seqtk", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqtk_nml", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml", + "Galaxy wrapper version": "1.0.1", + "Conda id": "seqtk", + "Conda version": "1.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "sistr_cmd", + "Galaxy tool ids": [ + "sistr_cmd" + ], + "Description": "SISTR in silico serotyping tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/sistr_cmd", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sistr_cmd", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd", + "Galaxy wrapper version": "1.1.1", + "Conda id": "sistr_cmd", + "Conda version": "1.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "smalt", + "Galaxy tool ids": [ + "smalt" + ], + "Description": "SMALT aligns DNA sequencing reads with a reference genome.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://www.sanger.ac.uk/science/tools/smalt-0", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "smalt", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://sourceforge.net/projects/smalt/", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt", + "Galaxy wrapper version": "0.7.6", + "Conda id": "smalt", + "Conda version": "0.7.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "spades_header_fixer", + "Galaxy tool ids": [ + "spades_header_fixer" + ], + "Description": "Fixes Spades Fasta ids", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/galaxy_tools", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "spades_fasta_header_fixer", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer", + "Galaxy wrapper version": "1.1.2+galaxy1", + "Conda id": "sed", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "spatyper", + "Galaxy tool ids": [ + "spatyper" + ], + "Description": "Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/HCGB-IGTP/spaTyper", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "spatyper", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper", + "Galaxy wrapper version": "0.3.3", + "Conda id": "spatyper", + "Conda version": "0.3.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "spolpred", + "Galaxy tool ids": [ + "spolpred" + ], + "Description": "A program for predicting the spoligotype from raw sequence reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "spolpred", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred", + "Galaxy wrapper version": "1.0.1", + "Conda id": "spolpred", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "srst2", + "Galaxy tool ids": [ + "srst2" + ], + "Description": "Short Read Sequence Typing for Bacterial Pathogens", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "srst2", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2", + "Galaxy wrapper version": "0.3.7", + "Conda id": "srst2", + "Conda version": "0.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "staramr", + "Galaxy tool ids": [ + "staramr_search" + ], + "Description": "Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/staramr", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "staramr", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr", + "Galaxy wrapper version": "0.10.0", + "Conda id": "staramr", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "stringmlst", + "Galaxy tool ids": [ + "stringmlst" + ], + "Description": "Rapid and accurate identification of the sequence type (ST)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "stringmlst", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst", + "Galaxy wrapper version": "1.1.0", + "Conda id": "stringMLST", + "Conda version": "0.6.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "tree_relabeler", + "Galaxy tool ids": [ + "tree_relabel" + ], + "Description": "Relabels the tips of a newick formatted tree.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "tree_relabeler", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler", + "Galaxy wrapper version": "1.1.0", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "wade", + "Galaxy tool ids": [ + "wade" + ], + "Description": "identify regions of interest", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/phac-nml/wade", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "wade", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/wade", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade", + "Galaxy wrapper version": "0.2.5+galaxy1", + "Conda id": "wade", + "Conda version": "0.2.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "camera", + "Galaxy tool ids": [ + "abims_CAMERA_annotateDiffreport", + "abims_CAMERA_combinexsAnnos" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "camera", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera", + "Galaxy wrapper version": "1.48.0", + "Conda id": "r-snow", + "Conda version": "0.4_1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 2, + "Tools available on UseGalaxy.org (Main)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "correlation_analysis", + "Galaxy tool ids": [ + "correlation_analysis" + ], + "Description": "[Metabolomics][W4M] Metabolites Correlation Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "correlation_analysis", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis", + "Galaxy wrapper version": "1.0.1+galaxy0", + "Conda id": "r-batch", + "Conda version": "1.1_4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "gcms2isocor", + "Galaxy tool ids": [ + "gcms2isocor" + ], + "Description": "Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/p2m2/p2m2tools", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "gcms2isocor", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor", + "Galaxy wrapper version": "0.2.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "genform", + "Galaxy tool ids": [ + "genform" + ], + "Description": "genform: generation of molecular formulas by high-resolution MS and MS/MS data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://sourceforge.net/projects/genform/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "genform", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform", + "Galaxy wrapper version": null, + "Conda id": "genform", + "Conda version": "r8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "influx_data_manager", + "Galaxy tool ids": [ + "influx_data_manager" + ], + "Description": "Handling influx_si data inputs in Galaxy workflows", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "influx_si_data_manager", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager", + "Galaxy wrapper version": "1.0.2", + "Conda id": "influx-si-data-manager", + "Conda version": "1.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "influx_si", + "Galaxy tool ids": [ + "influx_si" + ], + "Description": "metabolic flux estimation based on [in]stationary labeling", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/sgsokol/influx", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "influx_si", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si", + "Galaxy wrapper version": "7.0.1", + "Conda id": "influx_si", + "Conda version": "7.0.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "ipo", + "Galaxy tool ids": [ + "ipo4retgroup", + "ipo4xcmsSet" + ], + "Description": "[W4M][LC-MS] IPO", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/rietho/IPO", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "ipo", + "Galaxy wrapper owner": "lecorguille", + "Galaxy wrapper source": "https://github.com/rietho/IPO", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo", + "Galaxy wrapper version": "1.10.0", + "Conda id": "bioconductor-ipo", + "Conda version": "1.28.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "isoplot", + "Galaxy tool ids": [ + "isoplot" + ], + "Description": "Isoplot is a software for the visualisation of MS data from C13 labelling experiments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metabolomics", + "Visualization" + ], + "ToolShed id": "isoplot", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/llegregam/Isoplot/tree/main", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot", + "Galaxy wrapper version": "1.3.0+galaxy1", + "Conda id": "isoplot", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "kmd_hmdb_data_plot", + "Galaxy tool ids": [ + "kmd_hmdb_data_plot" + ], + "Description": "retrieves data from KMD HMDB API and produce plot and csv file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/workflow4metabolomics/tools-metabolomics", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "kmd_hmdb_data_plot", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot", + "Galaxy wrapper version": "1.0.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "mixmodel4repeated_measures", + "Galaxy tool ids": [ + "mixmodel4repeated_measures" + ], + "Description": "[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "mixmodel4repeated_measures", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures", + "Galaxy wrapper version": "3.1.0", + "Conda id": "r-lme4", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "ms2snoop", + "Galaxy tool ids": [ + "ms2snoop" + ], + "Description": "[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "ms2snoop", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop", + "Galaxy wrapper version": "2.2.1", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "nmr_annotation", + "Galaxy tool ids": [ + "NmrAnnotation" + ], + "Description": "[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "nmr_annotation", + "Galaxy wrapper owner": "marie-tremblay-metatoul", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/nmr_annotation", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation", + "Galaxy wrapper version": "3.0.0", + "Conda id": "r-batch", + "Conda version": "1.1_4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "nmr_annotation2d", + "Galaxy tool ids": [ + "2DNmrAnnotation" + ], + "Description": "[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "2dnmrannotation", + "Galaxy wrapper owner": "marie-tremblay-metatoul", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d", + "Galaxy wrapper version": "2.0.0", + "Conda id": "r-batch", + "Conda version": "1.1_4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "nmr_preprocessing", + "Galaxy tool ids": [ + "NMR_Preprocessing", + "NMR_Read" + ], + "Description": "[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "nmr_preprocessing", + "Galaxy wrapper owner": "marie-tremblay-metatoul", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/nmr_preprocessing", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing", + "Galaxy wrapper version": null, + "Conda id": "r-batch", + "Conda version": "1.1_4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 2, + "Tools available on UseGalaxy.org (Main)": 0, + "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": 2 + }, + { + "Galaxy wrapper id": "normalization", + "Galaxy tool ids": [ + "normalization" + ], + "Description": "[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://workflow4metabolomics.org", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "normalization", + "Galaxy wrapper owner": "marie-tremblay-metatoul", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/normalization", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization", + "Galaxy wrapper version": "1.0.7", + "Conda id": "r-batch", + "Conda version": "1.1_4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "physiofit", + "Galaxy tool ids": [ + "physiofit" + ], + "Description": "PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "physiofit.readthedocs.io", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "physiofit", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/MetaSys-LISBP/PhysioFit", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit", + "Galaxy wrapper version": "3.3.5", + "Conda id": "physiofit", + "Conda version": "3.3.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "physiofit_manager", + "Galaxy tool ids": [ + "physiofit_data_manager" + ], + "Description": "Handling of physiofit input files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "physiofit_manager", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager", + "Galaxy wrapper version": "1.0.1", + "Conda id": "physiofit_data_manager", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "skyline2isocor", + "Galaxy tool ids": [ + "skyline2isocor" + ], + "Description": "Converting skyline output to IsoCor input", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "skyline2isocor", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor", + "Galaxy wrapper version": "1.0.0", + "Conda id": "skyline2isocor", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": "xcms", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/sneumann/xcms", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "xcms", + "Galaxy wrapper owner": "workflow4metabolomics", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/", + "Galaxy wrapper parsed folder": "https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms", + "Galaxy wrapper version": "3.12.0", + "Conda id": "bioconductor-xcms", + "Conda version": "4.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 9, + "Available on UseGalaxy.org.au": 9, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.fr": 10, + "Tools available on UseGalaxy.org (Main)": 9, + "Tools available on UseGalaxy.org.au": 9, + "Tools available on UseGalaxy.eu": 10, + "Tools available on UseGalaxy.fr": 10, + "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": 6, + "Tools available on UseGalaxy.cz": 10, + "Tools available on UseGalaxy.no": 9 + }, + { + "Galaxy wrapper id": "apollo", + "Galaxy tool ids": [ + "create_account", + "feat_from_gff3", + "create_or_update", + "delete_features", + "delete_organism", + "export", + "fetch_jbrowse", + "iframe", + "list_organism" + ], + "Description": "Access an Apollo instance from Galaxy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxy-genome-annotation/python-apollo", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo", + "Galaxy wrapper version": null, + "Conda id": "apollo", + "Conda version": "4.2.13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 9, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 9, + "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)": 8, + "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": 9, + "Tools available on UseGalaxy.no": 9 + }, + { + "Galaxy wrapper id": "askomics", + "Galaxy tool ids": [ + "askomics_integrate" + ], + "Description": "Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/askomics/", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics", + "Galaxy wrapper version": null, + "Conda id": "askocli", + "Conda version": "0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "chado", + "Galaxy tool ids": [ + "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" + ], + "Description": "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", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxy-genome-annotation/python-chado", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado", + "Galaxy wrapper version": null, + "Conda id": "python-chado", + "Conda version": "2.3.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "genenotebook", + "Galaxy tool ids": [ + "genenotebook_build" + ], + "Description": "Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://genenotebook.github.io", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook", + "Galaxy wrapper version": "0.4.15", + "Conda id": "genoboo", + "Conda version": "0.4.15", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": "jbrowse", + "Galaxy tool ids": [ + "jbrowse_to_container" + ], + "Description": "A tool allowing to export a JBrowse dataset into a JBrowse docker container", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://jbrowse.org", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": "jbrowse_to_container", + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse", + "Galaxy wrapper version": null, + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "repeatexplorer2", + "Galaxy tool ids": [ + "repeatexplorer_clustering" + ], + "Description": "Tool for annotation of repeats from unassembled shotgun reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/repeatexplorer/repex_tarean", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "repeatexplorer2", + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2", + "Galaxy wrapper version": "2.3.8", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "tripal", + "Galaxy tool ids": [ + "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" + ], + "Description": "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", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxy-genome-annotation/python-tripal", + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "gga", + "Galaxy wrapper source": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal", + "Galaxy wrapper parsed folder": "https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal", + "Galaxy wrapper version": null, + "Conda id": "python-tripal", + "Conda version": "3.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "w4mcorcov", + "Galaxy tool ids": [ + "w4mcorcov" + ], + "Description": "OPLS-DA Contrasts of Univariate Results", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "w4mcorcov", + "Galaxy wrapper owner": "eschen42", + "Galaxy wrapper source": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master", + "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov", + "Galaxy wrapper version": "0.98.18", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "w4mclassfilter", + "Galaxy tool ids": [ + "w4mclassfilter" + ], + "Description": "Filter W4M data by values or metadata", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "w4mclassfilter", + "Galaxy wrapper owner": "eschen42", + "Galaxy wrapper source": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master", + "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter", + "Galaxy wrapper version": "0.98.19", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "w4mjoinpn", + "Galaxy tool ids": [ + "w4mjoinpn" + ], + "Description": "Join positive- and negative-mode W4M datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "w4mjoinpn", + "Galaxy wrapper owner": "eschen42", + "Galaxy wrapper source": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master", + "Galaxy wrapper parsed folder": "https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn", + "Galaxy wrapper version": "0.98.2", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "batched_lastz", + "Galaxy tool ids": [ + "batched_lastz" + ], + "Description": "Galaxy wrapper for the batching Lastz runs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/gsneha26/SegAlign", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "batched_lastz", + "Galaxy wrapper owner": "richard-burhans", + "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz", + "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz", + "Galaxy wrapper version": "1.04.22", + "Conda id": "lastz", + "Conda version": "1.04.22", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "ncbi_fcs_adaptor", + "Galaxy tool ids": [ + "ncbi_fcs_adaptor" + ], + "Description": "FCS-adaptor detects adaptor and vector contamination in genome sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ncbi/fcs", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ncbi_fcs_adaptor", + "Galaxy wrapper owner": "richard-burhans", + "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor", + "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor", + "Galaxy wrapper version": "0.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "segalign", + "Galaxy tool ids": [ + "segalign" + ], + "Description": "A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/gsneha26/SegAlign", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "segalign", + "Galaxy wrapper owner": "richard-burhans", + "Galaxy wrapper source": "https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign", + "Galaxy wrapper parsed folder": "https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign", + "Galaxy wrapper version": "0.1.2.2", + "Conda id": "segalign-full", + "Conda version": "0.1.2.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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__alignment", + "Galaxy tool ids": [ + "qiime2__alignment__mafft", + "qiime2__alignment__mafft_add", + "qiime2__alignment__mask" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-alignment", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 3, + "Tools available on UseGalaxy.org (Main)": 3, + "Tools available on UseGalaxy.org.au": 3, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 3, + "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": 3, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__composition", + "Galaxy tool ids": [ + "qiime2__composition__add_pseudocount", + "qiime2__composition__ancom", + "qiime2__composition__ancombc", + "qiime2__composition__da_barplot", + "qiime2__composition__tabulate" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-composition", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.fr": 2, + "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": 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": 4, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__cutadapt", + "Galaxy tool ids": [ + "qiime2__cutadapt__demux_paired", + "qiime2__cutadapt__demux_single", + "qiime2__cutadapt__trim_paired", + "qiime2__cutadapt__trim_single" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-cutadapt", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 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__dada2", + "Galaxy tool ids": [ + "qiime2__dada2__denoise_ccs", + "qiime2__dada2__denoise_paired", + "qiime2__dada2__denoise_pyro", + "qiime2__dada2__denoise_single" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://benjjneb.github.io/dada2/", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 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__deblur", + "Galaxy tool ids": [ + "qiime2__deblur__denoise_16S", + "qiime2__deblur__denoise_other", + "qiime2__deblur__visualize_stats" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/biocore/deblur", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 3, + "Tools available on UseGalaxy.org (Main)": 3, + "Tools available on UseGalaxy.org.au": 3, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 3, + "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": 3, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__demux", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-demux", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 6, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.fr": 6, + "Tools available on UseGalaxy.org (Main)": 6, + "Tools available on UseGalaxy.org.au": 6, + "Tools available on UseGalaxy.eu": 6, + "Tools available on UseGalaxy.fr": 6, + "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": 6, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__diversity", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-diversity", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 21, + "Available on UseGalaxy.org.au": 21, + "Available on UseGalaxy.eu": 21, + "Available on UseGalaxy.fr": 21, + "Tools available on UseGalaxy.org (Main)": 21, + "Tools available on UseGalaxy.org.au": 21, + "Tools available on UseGalaxy.eu": 21, + "Tools available on UseGalaxy.fr": 21, + "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": 21, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__diversity_lib", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-diversity-lib", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 12, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 12, + "Available on UseGalaxy.fr": 12, + "Tools available on UseGalaxy.org (Main)": 12, + "Tools available on UseGalaxy.org.au": 12, + "Tools available on UseGalaxy.eu": 12, + "Tools available on UseGalaxy.fr": 12, + "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": 12, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__emperor", + "Galaxy tool ids": [ + "qiime2__emperor__biplot", + "qiime2__emperor__plot", + "qiime2__emperor__procrustes_plot" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://emperor.microbio.me", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 3, + "Tools available on UseGalaxy.org (Main)": 3, + "Tools available on UseGalaxy.org.au": 3, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 3, + "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": 3, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__feature_classifier", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-feature-classifier", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 10, + "Available on UseGalaxy.org.au": 10, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.fr": 10, + "Tools available on UseGalaxy.org (Main)": 10, + "Tools available on UseGalaxy.org.au": 10, + "Tools available on UseGalaxy.eu": 10, + "Tools available on UseGalaxy.fr": 10, + "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": 10, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__feature_table", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-feature-table", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 17, + "Available on UseGalaxy.org.au": 17, + "Available on UseGalaxy.eu": 17, + "Available on UseGalaxy.fr": 17, + "Tools available on UseGalaxy.org (Main)": 17, + "Tools available on UseGalaxy.org.au": 17, + "Tools available on UseGalaxy.eu": 17, + "Tools available on UseGalaxy.fr": 17, + "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": 17, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__fragment_insertion", + "Galaxy tool ids": [ + "qiime2__fragment_insertion__classify_otus_experimental", + "qiime2__fragment_insertion__filter_features", + "qiime2__fragment_insertion__sepp" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-fragment-insertion", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 3, + "Tools available on UseGalaxy.org (Main)": 3, + "Tools available on UseGalaxy.org.au": 3, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 3, + "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": 3, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__longitudinal", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-longitudinal", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 11, + "Available on UseGalaxy.org.au": 11, + "Available on UseGalaxy.eu": 11, + "Available on UseGalaxy.fr": 11, + "Tools available on UseGalaxy.org (Main)": 11, + "Tools available on UseGalaxy.org.au": 11, + "Tools available on UseGalaxy.eu": 11, + "Tools available on UseGalaxy.fr": 11, + "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": 11, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__metadata", + "Galaxy tool ids": [ + "qiime2__metadata__distance_matrix", + "qiime2__metadata__merge", + "qiime2__metadata__shuffle_groups", + "qiime2__metadata__tabulate" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-metadata", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 3, + "Tools available on UseGalaxy.org (Main)": 3, + "Tools available on UseGalaxy.org.au": 3, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 3, + "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": 3, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__phylogeny", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-phylogeny", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 12, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 12, + "Available on UseGalaxy.fr": 12, + "Tools available on UseGalaxy.org (Main)": 12, + "Tools available on UseGalaxy.org.au": 12, + "Tools available on UseGalaxy.eu": 12, + "Tools available on UseGalaxy.fr": 12, + "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": 12, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__quality_control", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-quality-control", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 6, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.fr": 6, + "Tools available on UseGalaxy.org (Main)": 6, + "Tools available on UseGalaxy.org.au": 6, + "Tools available on UseGalaxy.eu": 6, + "Tools available on UseGalaxy.fr": 6, + "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": 6, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__quality_filter", + "Galaxy tool ids": [ + "qiime2__quality_filter__q_score" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-quality-filter", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "suite_qiime2__rescript", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nbokulich/RESCRIPt", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-sample-classifier", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 15, + "Available on UseGalaxy.org.au": 15, + "Available on UseGalaxy.eu": 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", + "Galaxy tool ids": [ + "qiime2__taxa__barplot", + "qiime2__taxa__collapse", + "qiime2__taxa__filter_seqs", + "qiime2__taxa__filter_table" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-taxa", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 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", + "Galaxy tool ids": [ + "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" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/qiime2/q2-vsearch", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch", + "Galaxy wrapper version": "2024.5.0+q2galaxy.2024.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 8, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 8, + "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", + "Galaxy tool ids": [ + "qiime2_core__tools__export", + "qiime2_core__tools__import", + "qiime2_core__tools__import_fastq" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://qiime2.org", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools", + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools", + "Galaxy wrapper version": "2024.5.0+dist.he540b0b0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 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", + "Galaxy tool ids": [], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics", + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "q2d2", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "add_value", + "Galaxy tool ids": [ + "addValue" + ], + "Description": "Add a value as a new column.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "add_value", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value", + "Galaxy wrapper version": "1.0.1", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "annotation_profiler", + "Galaxy tool ids": [ + "Annotation_Profiler_0" + ], + "Description": "Profile Annotations for a set of genomic intervals", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "annotation_profiler", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "best_regression_subsets", + "Galaxy tool ids": [ + "BestSubsetsRegression1" + ], + "Description": "Perform Best-subsets Regression", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "best_regression_subsets", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets", + "Galaxy wrapper version": "1.0.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "blat_coverage_report", + "Galaxy tool ids": [ + "generate_coverage_report" + ], + "Description": "Polymorphism of the Reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers", + "Sequence Analysis" + ], + "ToolShed id": "blat_coverage_report", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "blat_mapping", + "Galaxy tool ids": [ + "blat2wig" + ], + "Description": "Coverage of the Reads in wiggle format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers", + "Sequence Analysis" + ], + "ToolShed id": "blat_mapping", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "bowtie_wrappers", + "Galaxy tool ids": [ + "bowtie_wrapper" + ], + "Description": "Galaxy wrappers for the Bowtie short read mapping tools.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bowtie-bio.sourceforge.net/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "bowtie_wrappers", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers", + "Galaxy wrapper version": "1.2.0", + "Conda id": "bowtie", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "canonical_correlation_analysis", + "Galaxy tool ids": [ + "cca1" + ], + "Description": "Canonical Correlation Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "canonical_correlation_analysis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis", + "Galaxy wrapper version": "1.0.0", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "categorize_elements_satisfying_criteria", + "Galaxy tool ids": [ + "categorize_elements_satisfying_criteria" + ], + "Description": "Categorize Elements satisfying criteria.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "categorize_elements_satisfying_criteria", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "ccat", + "Galaxy tool ids": [ + "peakcalling_ccat" + ], + "Description": "Control-based ChIP-seq Analysis Tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "ccat", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat", + "Galaxy wrapper version": "0.0.2", + "Conda id": "ccat", + "Conda version": "3.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cd_hit_dup", + "Galaxy tool ids": [ + "cd_hit_dup" + ], + "Description": "simple tool for removing duplicates from sequencing reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": "cd_hit_dup", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup", + "Galaxy wrapper version": "0.0.1", + "Conda id": "cd-hit-auxtools", + "Conda version": "4.8.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": 1, + "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": "change_case", + "Galaxy tool ids": [ + "ChangeCase" + ], + "Description": "Convert column case.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "change_case", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case", + "Galaxy wrapper version": "1.0.1", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "compute_motif_frequencies_for_all_motifs", + "Galaxy tool ids": [ + "compute_motif_frequencies_for_all_motifs" + ], + "Description": "Compute Motif Frequencies For All Motifs, motif by motif.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": "compute_motif_frequencies_for_all_motifs", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "compute_motifs_frequency", + "Galaxy tool ids": [ + "compute_motifs_frequency" + ], + "Description": "Compute Motif Frequencies in indel flanking regions.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": "compute_motifs_frequency", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "compute_q_values", + "Galaxy tool ids": [ + "compute_q_values" + ], + "Description": "Compute q-values based on multiple simultaneous tests p-values", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "compute_q_values", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "condense_characters", + "Galaxy tool ids": [ + "Condense characters1" + ], + "Description": "Condense consecutive characters.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "condense_characters", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "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": 1, + "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": 1, + "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": "convert_characters", + "Galaxy tool ids": [ + "Convert characters1" + ], + "Description": "Convert delimiters to tab.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "convert_characters", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 1, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "convert_solid_color2nuc", + "Galaxy tool ids": [ + "color2nuc" + ], + "Description": "Convert Color Space to Nucleotides", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "convert_solid_color2nuc", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "correlation", + "Galaxy tool ids": [ + "cor2" + ], + "Description": "Correlation for numeric columns", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "correlation", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "count_gff_features", + "Galaxy tool ids": [ + "count_gff_features" + ], + "Description": "Count GFF Features", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "count_gff_features", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features", + "Galaxy wrapper version": "0.2", + "Conda id": "galaxy-ops", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "ctd_batch", + "Galaxy tool ids": [ + "ctdBatch_1" + ], + "Description": "CTD analysis of chemicals, diseases, or genes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ctd_batch", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cummerbund", + "Galaxy tool ids": [ + "cummeRbund" + ], + "Description": "Wrapper for the Bioconductor cummeRbund library", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/cummeRbund.html", + "ToolShed categories": [ + "RNA", + "Visualization" + ], + "ToolShed id": "cummerbund", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund", + "Galaxy wrapper version": "2.16.0", + "Conda id": "fonts-conda-ecosystem", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cummerbund_to_tabular", + "Galaxy tool ids": [ + "cummerbund_to_cuffdiff" + ], + "Description": "Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats", + "Next Gen Mappers" + ], + "ToolShed id": "cummerbund_to_tabular", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular", + "Galaxy wrapper version": "1.0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cut_columns", + "Galaxy tool ids": [ + "Cut1" + ], + "Description": "Select columns from a dataset.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "cut_columns", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns", + "Galaxy wrapper version": "1.0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "delete_overlapping_indels", + "Galaxy tool ids": [ + "delete_overlapping_indels" + ], + "Description": "Delete Overlapping Indels from a chromosome indels file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "delete_overlapping_indels", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "dgidb_annotator", + "Galaxy tool ids": [ + "dgidb_annotate" + ], + "Description": "Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Systems Biology", + "Variant Analysis" + ], + "ToolShed id": "dgidb_annotator", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "divide_pg_snp", + "Galaxy tool ids": [ + "dividePgSnp" + ], + "Description": "Separate pgSnp alleles into columns", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "divide_pg_snp", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "draw_stacked_barplots", + "Galaxy tool ids": [ + "draw_stacked_barplots" + ], + "Description": "Draw Stacked Bar Plots for different categories and different criteria", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "draw_stacked_barplots", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots", + "Galaxy wrapper version": "1.0.0", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "dwt_cor_ava_perclass", + "Galaxy tool ids": [ + "compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" + ], + "Description": "Compute P-values and Correlation Coefficients for Feature Occurrences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "dwt_cor_ava_perclass", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass", + "Galaxy wrapper version": "1.0.1", + "Conda id": "r-waveslim", + "Conda version": "1.7.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "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": "dwt_cor_avb_all", + "Galaxy tool ids": [ + "compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" + ], + "Description": "Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "dwt_cor_avb_all", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all", + "Galaxy wrapper version": "1.0.1", + "Conda id": "r-waveslim", + "Conda version": "1.7.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "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": "dwt_ivc_all", + "Galaxy tool ids": [ + "compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" + ], + "Description": "Compute P-values and Second Moments for Feature Occurrences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "dwt_ivc_all", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all", + "Galaxy wrapper version": "1.0.1", + "Conda id": "r-waveslim", + "Conda version": "1.7.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "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": "dwt_var_perclass", + "Galaxy tool ids": [ + "compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" + ], + "Description": "Compute P-values and Max Variances for Feature Occurrences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "dwt_var_perclass", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass", + "Galaxy wrapper version": "1.0.1", + "Conda id": "r-waveslim", + "Conda version": "1.7.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "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": "dwt_var_perfeature", + "Galaxy tool ids": [ + "dwt_var1" + ], + "Description": "Wavelet variance using Discrete Wavelet Transfoms", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "dwt_var_perfeature", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature", + "Galaxy wrapper version": "1.0.2", + "Conda id": "r-bitops", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "express", + "Galaxy tool ids": [ + "express" + ], + "Description": "Quantify the abundances of a set of target sequences from sampled subsequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "express", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/express", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/express", + "Galaxy wrapper version": "1.1.1", + "Conda id": "eXpress", + "Conda version": "1.5.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fasta_compute_length", + "Galaxy tool ids": [ + "fasta_compute_length" + ], + "Description": "Compute sequence length", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_compute_length", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length", + "Galaxy wrapper version": "1.0.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fasta_concatenate_by_species", + "Galaxy tool ids": [ + "fasta_concatenate0" + ], + "Description": "Concatenate FASTA alignment by species", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_concatenate_by_species", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species", + "Galaxy wrapper version": "0.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fasta_filter_by_length", + "Galaxy tool ids": [ + "fasta_filter_by_length" + ], + "Description": "Filter sequences by length", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_filter_by_length", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length", + "Galaxy wrapper version": "1.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fasta_to_tabular", + "Galaxy tool ids": [ + "fasta2tab" + ], + "Description": "FASTA-to-Tabular converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_to_tabular", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular", + "Galaxy wrapper version": "1.1.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fastq_trimmer_by_quality", + "Galaxy tool ids": [ + "fastq_quality_trimmer" + ], + "Description": "FASTQ Quality Trimmer by sliding window", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_trimmer_by_quality", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fastqsolexa_to_fasta_qual", + "Galaxy tool ids": [ + "fastqsolexa_to_fasta_qual" + ], + "Description": "FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats", + "Fastq Manipulation" + ], + "ToolShed id": "fastqsolexa_to_fasta_qual", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "featurecounter", + "Galaxy tool ids": [ + "featureCoverage1" + ], + "Description": "Feature coverage", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "featurecounter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter", + "Galaxy wrapper version": "2.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "filter_transcripts_via_tracking", + "Galaxy tool ids": [ + "filter_combined_via_tracking" + ], + "Description": "Filter Combined Transcripts", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "filter_transcripts_via_tracking", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "generate_pc_lda_matrix", + "Galaxy tool ids": [ + "generate_matrix_for_pca_and_lda1" + ], + "Description": "Generate a Matrix for using PC and LDA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "generate_pc_lda_matrix", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "getindelrates_3way", + "Galaxy tool ids": [ + "indelRates_3way" + ], + "Description": "Estimate Indel Rates for 3-way alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "getindelrates_3way", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "getindels_2way", + "Galaxy tool ids": [ + "getIndels_2way" + ], + "Description": "Fetch Indels from pairwise alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "getindels_2way", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way", + "Galaxy wrapper version": "1.0.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "gmaj", + "Galaxy tool ids": [ + "gmaj_1" + ], + "Description": "GMAJ Multiple Alignment Viewer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "gmaj", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj", + "Galaxy wrapper version": "2.0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "hisat", + "Galaxy tool ids": [ + "hisat" + ], + "Description": "HISAT is a fast and sensitive spliced alignment program.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://ccb.jhu.edu/software/hisat/index.shtml", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hisat", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat", + "Galaxy wrapper version": "1.0.3", + "Conda id": "hisat", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "histogram", + "Galaxy tool ids": [ + "histogram_rpy" + ], + "Description": "Histogram of a numeric column", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "histogram", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram", + "Galaxy wrapper version": "1.0.4", + "Conda id": "rpy2", + "Conda version": "2.7.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "indels_3way", + "Galaxy tool ids": [ + "indels_3way" + ], + "Description": "Fetch Indels from 3-way alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "indels_3way", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way", + "Galaxy wrapper version": "1.0.3", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "kernel_canonical_correlation_analysis", + "Galaxy tool ids": [ + "kcca1" + ], + "Description": "Kernel Canonical Correlation Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "kernel_canonical_correlation_analysis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "kernel_principal_component_analysis", + "Galaxy tool ids": [ + "kpca1" + ], + "Description": "Kernel Principal Component Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "kernel_principal_component_analysis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "lastz_paired_reads", + "Galaxy tool ids": [ + "lastz_paired_reads_wrapper" + ], + "Description": "Galaxy wrapper for the Lastz alignment tool on paired reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "lastz_paired_reads", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads", + "Galaxy wrapper version": "1.1.1", + "Conda id": "lastz", + "Conda version": "1.04.22", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "lda_analysis", + "Galaxy tool ids": [ + "lda_analy1" + ], + "Description": "Perform Linear Discriminant Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "lda_analysis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "linear_regression", + "Galaxy tool ids": [ + "LinearRegression1" + ], + "Description": "Perform Linear Regression", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "linear_regression", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "logistic_regression_vif", + "Galaxy tool ids": [ + "LogisticRegression" + ], + "Description": "Perform Logistic Regression with vif", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis", + "Statistics" + ], + "ToolShed id": "logistic_regression_vif", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif", + "Galaxy wrapper version": "1.0.1", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "maf_cpg_filter", + "Galaxy tool ids": [ + "cpgFilter" + ], + "Description": "Mask CpG/non-CpG sites from MAF file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "maf_cpg_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "mapping_to_ucsc", + "Galaxy tool ids": [ + "mapToUCSC" + ], + "Description": "Format mapping data as UCSC custom track", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Visualization", + "Convert Formats", + "Next Gen Mappers" + ], + "ToolShed id": "mapping_to_ucsc", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "megablast_xml_parser", + "Galaxy tool ids": [ + "megablast_xml_parser" + ], + "Description": "Parse blast XML output", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers", + "Convert Formats" + ], + "ToolShed id": "megablast_xml_parser", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "merge_cols", + "Galaxy tool ids": [ + "mergeCols1" + ], + "Description": "Merge columns together.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "merge_cols", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols", + "Galaxy wrapper version": "1.0.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "microsatellite_birthdeath", + "Galaxy tool ids": [ + "microsatellite_birthdeath" + ], + "Description": "Identify microsatellite births and deaths", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "microsatellite_birthdeath", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "microsats_alignment_level", + "Galaxy tool ids": [ + "microsats_align1" + ], + "Description": "Extract Orthologous Microsatellites from pair-wise alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "microsats_alignment_level", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level", + "Galaxy wrapper version": "1.0.0", + "Conda id": "sputnik", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "microsats_mutability", + "Galaxy tool ids": [ + "microsats_mutability1" + ], + "Description": "Estimate microsatellite mutability by specified attributes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "microsats_mutability", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability", + "Galaxy wrapper version": "1.1.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "mine", + "Galaxy tool ids": [ + "maximal_information_based_nonparametric_exploration" + ], + "Description": "Maximal Information-based Nonparametric Exploration", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "mine", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine", + "Galaxy wrapper version": "0.0.1", + "Conda id": "MINE", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "multispecies_orthologous_microsats", + "Galaxy tool ids": [ + "multispecies_orthologous_microsats" + ], + "Description": "Extract orthologous microsatellites", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "multispecies_orthologous_microsats", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-sputnik", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "mutate_snp_codon", + "Galaxy tool ids": [ + "mutate_snp_codon_1" + ], + "Description": "Mutate Codons with SNPs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "mutate_snp_codon", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "partialr_square", + "Galaxy tool ids": [ + "partialRsq" + ], + "Description": "Compute partial R square", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "partialr_square", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square", + "Galaxy wrapper version": "1.0.0", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "pearson_correlation", + "Galaxy tool ids": [ + "Pearson_and_apos_Correlation1" + ], + "Description": "Pearson and apos Correlation between any two numeric columns", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "pearson_correlation", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pgsnp2gd_snp", + "Galaxy tool ids": [ + "pgSnp2gd_snp" + ], + "Description": "Convert from pgSnp to gd_snp", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pgsnp2gd_snp", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pileup_interval", + "Galaxy tool ids": [ + "pileup_interval" + ], + "Description": "Pileup-to-Interval condenses pileup format into ranges of bases", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "pileup_interval", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval", + "Galaxy wrapper version": "1.0.3", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "pileup_parser", + "Galaxy tool ids": [ + "pileup_parser" + ], + "Description": "Filter pileup on coverage and SNPs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-devteam/", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "pileup_parser", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser", + "Galaxy wrapper version": "1.0.2", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "plot_from_lda", + "Galaxy tool ids": [ + "plot_for_lda_output1" + ], + "Description": "Draw ROC plot on \"Perform LDA\" output", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "plot_from_lda", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "principal_component_analysis", + "Galaxy tool ids": [ + "pca1" + ], + "Description": "Principal Component Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "principal_component_analysis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis", + "Galaxy wrapper version": "1.0.2", + "Conda id": "rpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "quality_filter", + "Galaxy tool ids": [ + "qualityFilter" + ], + "Description": "Filter nucleotides based on quality scores", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "quality_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter", + "Galaxy wrapper version": "1.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "rcve", + "Galaxy tool ids": [ + "rcve1" + ], + "Description": "Compute RCVE", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "rcve", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve", + "Galaxy wrapper version": "1.0.0", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "remove_beginning", + "Galaxy tool ids": [ + "Remove beginning1" + ], + "Description": "Remove lines from the beginning of a file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "remove_beginning", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rmap", + "Galaxy tool ids": [ + "rmap_wrapper" + ], + "Description": "RMAP for Solexa Short Reads Alignment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "rmap", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rmap", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "rmapq", + "Galaxy tool ids": [ + "rmapq_wrapper" + ], + "Description": "RMAPQ for Solexa Short Reads Alignment with Quality Scores", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "rmapq", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rmap", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "sam2interval", + "Galaxy tool ids": [ + "sam2interval" + ], + "Description": "Convert SAM to interval.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "sam2interval", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval", + "Galaxy wrapper version": "1.0.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "sam_bitwise_flag_filter", + "Galaxy tool ids": [ + "sam_bw_filter" + ], + "Description": "Filter SAM on bitwise flag values", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "sam_bitwise_flag_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 0, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "scatterplot", + "Galaxy tool ids": [ + "scatterplot_rpy" + ], + "Description": "Scatterplot of two numeric columns", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "scatterplot", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot", + "Galaxy wrapper version": "1.0.3", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "short_reads_figure_high_quality_length", + "Galaxy tool ids": [ + "hist_high_quality_score" + ], + "Description": "Histogram of high quality score reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Graphics" + ], + "ToolShed id": "short_reads_figure_high_quality_length", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length", + "Galaxy wrapper version": "1.0.0", + "Conda id": "rpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "short_reads_figure_score", + "Galaxy tool ids": [ + "quality_score_distribution" + ], + "Description": "Build base quality distribution", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Graphics" + ], + "ToolShed id": "short_reads_figure_score", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score", + "Galaxy wrapper version": "1.0.2", + "Conda id": "fontconfig", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "short_reads_trim_seq", + "Galaxy tool ids": [ + "trim_reads" + ], + "Description": "Select high quality segments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "short_reads_trim_seq", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "show_beginning", + "Galaxy tool ids": [ + "Show beginning1" + ], + "Description": "Select lines from the beginning of a file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "show_beginning", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "show_tail", + "Galaxy tool ids": [ + "Show tail1" + ], + "Description": "Select lines from the end of a file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "show_tail", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 0, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 0, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "sicer", + "Galaxy tool ids": [ + "peakcalling_sicer" + ], + "Description": "Statistical approach for the Identification of ChIP-Enriched Regions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://home.gwu.edu/~wpeng/Software.htm", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "sicer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer", + "Galaxy wrapper version": "1.1", + "Conda id": "SICER", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "split_paired_reads", + "Galaxy tool ids": [ + "split_paired_reads" + ], + "Description": "Split paired end reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "split_paired_reads", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "substitution_rates", + "Galaxy tool ids": [ + "subRate1" + ], + "Description": "Estimate substitution rates for non-coding regions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "substitution_rates", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "substitutions", + "Galaxy tool ids": [ + "substitutions1" + ], + "Description": "Fetch substitutions from pairwise alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "substitutions", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions", + "Galaxy wrapper version": "1.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "t_test_two_samples", + "Galaxy tool ids": [ + "t_test_two_samples" + ], + "Description": "T Test for Two Samples", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "t_test_two_samples", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "table_annovar", + "Galaxy tool ids": [ + "table_annovar" + ], + "Description": "Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "table_annovar", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar", + "Galaxy wrapper version": "0.2", + "Conda id": "annovar", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "tabular_to_fasta", + "Galaxy tool ids": [ + "tab2fasta" + ], + "Description": "Tabular-to-FASTA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "tabular_to_fasta", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta", + "Galaxy wrapper version": "1.1.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "tophat", + "Galaxy tool ids": [ + "tophat" + ], + "Description": "Tophat for Illumina", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA", + "Next Gen Mappers" + ], + "ToolShed id": "tophat", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat", + "Galaxy wrapper version": "1.5.0", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "tophat2", + "Galaxy tool ids": [ + "tophat2" + ], + "Description": "Tophat - fast splice junction mapper for RNA-Seq reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://ccb.jhu.edu/software/tophat/index.shtml", + "ToolShed categories": [ + "RNA", + "Next Gen Mappers" + ], + "ToolShed id": "tophat2", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2", + "Galaxy wrapper version": "2.1.1", + "Conda id": "bowtie2", + "Conda version": "2.5.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "tophat_fusion_post", + "Galaxy tool ids": [ + "tophat_fusion_post" + ], + "Description": "Wrapper for Tophat-Fusion post step", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "tophat_fusion_post", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post", + "Galaxy wrapper version": "0.1", + "Conda id": "blast+", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "trimmer", + "Galaxy tool ids": [ + "trimmer" + ], + "Description": "Trim leading or trailing characters.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "trimmer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer", + "Galaxy wrapper version": "0.0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 1, + "Tools available on ARGs-OAP": 1, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 1, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "Tools available on ChemFlow": 0, + "Tools available on Coloc-stats": 1, + "Tools available on CorGAT": 1, + "Tools available on CropGalaxy": 1, + "Tools available on Dintor": 1, + "Tools available on FreeBioinfo": 0, + "Tools available on GASLINI": 1, + "Tools available on Galaxy@AuBi": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 1, + "Tools available on GigaGalaxy": 1, + "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": 1, + "Tools available on Mandoiu Lab": 0, + "Tools available on MiModD NacreousMap": 0, + "Tools available on Oqtans": 1, + "Tools available on Palfinder": 0, + "Tools available on PepSimili": 1, + "Tools available on PhagePromotor": 1, + "Tools available on Protologger": 0, + "Tools available on UseGalaxy.be": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "ucsc_custom_track", + "Galaxy tool ids": [ + "build_ucsc_custom_track_1" + ], + "Description": "Build custom track for UCSC genome browser", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ucsc_custom_track", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "varscan_version_2", + "Galaxy tool ids": [ + "varscan" + ], + "Description": "VarScan wrapper", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://dkoboldt.github.io/varscan/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "varscan_version_2", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2", + "Galaxy wrapper version": "2.4.2", + "Conda id": "varscan", + "Conda version": "2.4.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcf2pgsnp", + "Galaxy tool ids": [ + "vcf2pgSnp" + ], + "Description": "VCF to pgSnp", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcf2pgsnp", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcf_annotate", + "Galaxy tool ids": [ + "vcf_annotate" + ], + "Description": "Annotate a VCF file (dbSNP, hapmap)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcf_annotate", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "vcf_extract", + "Galaxy tool ids": [ + "vcf_extract" + ], + "Description": "Extract reads from a specified region", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcf_extract", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "vcf_filter", + "Galaxy tool ids": [ + "vcf_filter" + ], + "Description": "Filter a VCF file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcf_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcf_intersect", + "Galaxy tool ids": [ + "vcf_intersect" + ], + "Description": "Generate the intersection of two VCF files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcf_intersect", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": 1, + "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": "weightedaverage", + "Galaxy tool ids": [ + "wtavg" + ], + "Description": "Assign weighted-average of the values of features overlapping an interval", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "weightedaverage", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage", + "Galaxy wrapper version": "1.0.1", + "Conda id": "galaxy-ops", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "windowsplitter", + "Galaxy tool ids": [ + "winSplitter" + ], + "Description": "Make windows", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "windowsplitter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter", + "Galaxy wrapper version": "1.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "xy_plot", + "Galaxy tool ids": [ + "XY_Plot_1" + ], + "Description": "Plotting tool for multiple series and graph types", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Statistics" + ], + "ToolShed id": "xy_plot", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot", + "Galaxy wrapper version": "1.0.2", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "basecoverage", + "Galaxy tool ids": [ + "gops_basecoverage_1" + ], + "Description": "Base Coverage of all intervals", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "basecoverage", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cluster", + "Galaxy tool ids": [ + "gops_cluster_1" + ], + "Description": "Cluster the intervals of a dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "cluster", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "complement", + "Galaxy tool ids": [ + "gops_complement_1" + ], + "Description": "Complement intervals of a dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "complement", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "concat", + "Galaxy tool ids": [ + "gops_concat_1" + ], + "Description": "Concatenate two bed files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "concat", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat", + "Galaxy wrapper version": "1.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "coverage", + "Galaxy tool ids": [ + "gops_coverage_1" + ], + "Description": "Coverage of a set of intervals on second set of intervals", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "coverage", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "flanking_features", + "Galaxy tool ids": [ + "flanking_features_1" + ], + "Description": "Fetch closest non-overlapping feature for every interval", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "flanking_features", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features", + "Galaxy wrapper version": "4.0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "get_flanks", + "Galaxy tool ids": [ + "get_flanks1" + ], + "Description": "Get flanks returns flanking region/s for every gene", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "get_flanks", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "intersect", + "Galaxy tool ids": [ + "gops_intersect_1" + ], + "Description": "Intersect the intervals of two datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "intersect", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "join", + "Galaxy tool ids": [ + "gops_join_1" + ], + "Description": "Join the intervals of two datasets side-by-side", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "join", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "merge", + "Galaxy tool ids": [ + "gops_merge_1" + ], + "Description": "Merge the overlapping intervals of a dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "merge", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "subtract", + "Galaxy tool ids": [ + "gops_subtract_1" + ], + "Description": "Subtract the intervals of two datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "subtract", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "subtract_query", + "Galaxy tool ids": [ + "subtract_query1" + ], + "Description": "Subtract Whole Dataset from another dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "subtract_query", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query", + "Galaxy wrapper version": "0.1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "tables_arithmetic_operations", + "Galaxy tool ids": [ + "tables_arithmetic_operations" + ], + "Description": "Arithmetic Operations on tables", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/gops", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "tables_arithmetic_operations", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations", + "Galaxy wrapper version": "1.0.0", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "hgv_fundo", + "Galaxy tool ids": [ + "hgv_funDo" + ], + "Description": "FunDO human genes associated with disease terms", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "hgv_fundo", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "hgv_hilbertvis", + "Galaxy tool ids": [ + "hgv_hilbertvis" + ], + "Description": "HVIS visualization of genomic data with the Hilbert curve", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ebi.ac.uk/huber-srv/hilbert/", + "ToolShed categories": [ + "Graphics", + "Visualization" + ], + "ToolShed id": "hgv_hilbertvis", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis", + "Galaxy wrapper version": "1.0.0", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "snpfreq", + "Galaxy tool ids": [ + "hgv_snpFreq" + ], + "Description": "snpFreq significant SNPs in case-control data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis", + "Statistics" + ], + "ToolShed id": "snpfreq", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq", + "Galaxy wrapper version": "1.0.1", + "Conda id": "R", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "find_diag_hits", + "Galaxy tool ids": [ + "find_diag_hits" + ], + "Description": "Find diagnostic hits", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "find_diag_hits", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits", + "Galaxy wrapper version": "1.0.0", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "gi2taxonomy", + "Galaxy tool ids": [ + "Fetch Taxonomic Ranks" + ], + "Description": "Fetch taxonomic representation", + "bio.tool id": "gi2taxonomy", + "bio.tool ids": [ + "gi2taxonomy" + ], + "biii": null, + "bio.tool name": "gi2taxonomy", + "bio.tool description": "The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).", + "EDAM operation": [ + "Database search", + "ID mapping" + ], + "EDAM topic": [ + "Taxonomy" + ], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "gi2taxonomy", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy", + "Galaxy wrapper version": "1.1.1", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [ + "Database search", + "ID mapping" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "kraken2tax", + "Galaxy tool ids": [ + "Kraken2Tax" + ], + "Description": "Convert Kraken output to Galaxy taxonomy data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kraken2tax", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax", + "Galaxy wrapper version": "1.2+galaxy0", + "Conda id": "gawk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "lca_wrapper", + "Galaxy tool ids": [ + "lca1" + ], + "Description": "Find lowest diagnostic rank", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "lca_wrapper", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper", + "Galaxy wrapper version": "1.0.1", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "poisson2test", + "Galaxy tool ids": [ + "poisson2test" + ], + "Description": "Poisson two-sample test", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Statistics", + "Metagenomics" + ], + "ToolShed id": "poisson2test", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test", + "Galaxy wrapper version": "1.0.0", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "t2ps", + "Galaxy tool ids": [ + "Draw_phylogram" + ], + "Description": "Draw phylogeny", + "bio.tool id": "t2ps", + "bio.tool ids": [ + "t2ps" + ], + "biii": null, + "bio.tool name": "Draw phylogeny", + "bio.tool description": "\"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format.\" - Galaxy tool wrapper", + "EDAM operation": [ + "Phylogenetic tree visualisation" + ], + "EDAM topic": [ + "Phylogenomics" + ], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "t2ps", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps", + "Galaxy wrapper version": "1.0.0", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [ + "Phylogenetic tree visualisation" + ], + "EDAM topic (no superclasses)": [ + "Phylogenomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "t2t_report", + "Galaxy tool ids": [ + "t2t_report" + ], + "Description": "Summarize taxonomy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/natefoo/taxonomy", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "t2t_report", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report", + "Galaxy wrapper version": "1.0.0", + "Conda id": "taxonomy", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_annotate", + "Galaxy tool ids": [ + "vcftools_annotate" + ], + "Description": "Annotate VCF using custom/user-defined annotations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_annotate", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate", + "Galaxy wrapper version": "0.1", + "Conda id": "echo", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_compare", + "Galaxy tool ids": [ + "vcftools_compare" + ], + "Description": "Compare VCF files to get overlap and uniqueness statistics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_compare", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare", + "Galaxy wrapper version": "0.1", + "Conda id": "tabix", + "Conda version": "1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_consensus", + "Galaxy tool ids": [ + "vcftools_consensus" + ], + "Description": "Apply VCF variants to a fasta file to create consensus sequence", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_consensus", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus", + "Galaxy wrapper version": "0.1.11", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "vcftools_isec", + "Galaxy tool ids": [ + "vcftools_isec" + ], + "Description": "Intersect multiple VCF datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_isec", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec", + "Galaxy wrapper version": "0.1.1", + "Conda id": "tabix", + "Conda version": "1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_merge", + "Galaxy tool ids": [ + "vcftools_merge" + ], + "Description": "Merge multiple VCF datasets into a single dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_merge", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge", + "Galaxy wrapper version": "0.1.11", + "Conda id": "tabix", + "Conda version": "1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_slice", + "Galaxy tool ids": [ + "vcftools_slice" + ], + "Description": "Subset VCF dataset by genomic regions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_slice", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice", + "Galaxy wrapper version": "0.1", + "Conda id": "echo", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vcftools_subset", + "Galaxy tool ids": [ + "vcftools_subset" + ], + "Description": "Select samples from a VCF dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://vcftools.github.io/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcftools_subset", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset", + "Galaxy wrapper version": "0.1", + "Conda id": "tabix", + "Conda version": "1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "10x_bamtofastq", + "Galaxy tool ids": [ + "10x_bamtofastq" + ], + "Description": "Converts 10x Genomics BAM to FASTQ", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/10XGenomics/bamtofastq", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "10x_bamtofastq", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq", + "Galaxy wrapper version": "1.4.1", + "Conda id": "10x_bamtofastq", + "Conda version": "1.4.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "AggregateAlignments", + "Galaxy tool ids": [ + "graphclust_aggregate_alignments" + ], + "Description": "Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_aggregate_alignments", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments", + "Galaxy wrapper version": "0.6.0", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "AlignCluster", + "Galaxy tool ids": [ + "graphclust_align_cluster" + ], + "Description": "Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_align_cluster", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster", + "Galaxy wrapper version": "0.1", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1 + }, + { + "Galaxy wrapper id": "CMFinder", + "Galaxy tool ids": [ + "cmFinder" + ], + "Description": "Determines consensus motives for sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_cmfinder", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder", + "Galaxy wrapper version": "0.4", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "CollectResults", + "Galaxy tool ids": [ + "glob_report" + ], + "Description": "Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_postprocessing", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults", + "Galaxy wrapper version": "0.5", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "CollectResultsNoAlign", + "Galaxy tool ids": [ + "graphclust_glob_report_no_align" + ], + "Description": "Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_postprocessing_no_align", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign", + "Galaxy wrapper version": "0.5", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "GSPAN", + "Galaxy tool ids": [ + "gspan" + ], + "Description": "Second step of GraphClust", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_fasta_to_gspan", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN", + "Galaxy wrapper version": "0.4", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "LocARNAGraphClust", + "Galaxy tool ids": [ + "locarna_best_subtree" + ], + "Description": "MLocARNA computes a multiple sequence-structure alignment of RNA sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_mlocarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust", + "Galaxy wrapper version": "0.4", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "NSPDK", + "Galaxy tool ids": [ + "NSPDK_candidateClust", + "nspdk_sparse" + ], + "Description": "Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_nspdk", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK", + "Galaxy wrapper version": "9.2.3.1", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 2, + "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": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "Plotting", + "Galaxy tool ids": [ + "motifFinderPlot" + ], + "Description": "Plotting results for GraphClust", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_motif_finder_plot", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting", + "Galaxy wrapper version": "0.4", + "Conda id": "seaborn", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "PrepareForMlocarna", + "Galaxy tool ids": [ + "preMloc" + ], + "Description": "This tool prepares files for locarna step.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_prepocessing_for_mlocarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna", + "Galaxy wrapper version": "0.4", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "Preprocessing", + "Galaxy tool ids": [ + "preproc" + ], + "Description": "Preprocessing input for GraphClust", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust_preprocessing", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing", + "Galaxy wrapper version": "0.5", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "Structure_GSPAN", + "Galaxy tool ids": [ + "structure_to_gspan" + ], + "Description": "Convert RNA structure to GSPAN graphs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "structure_to_gspan", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN", + "Galaxy wrapper version": "0.4", + "Conda id": "graphclust-wrappers", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "agat", + "Galaxy tool ids": [ + "agat" + ], + "Description": "GTF/GFF analysis toolkit", + "bio.tool id": "agat", + "bio.tool ids": [ + "agat" + ], + "biii": null, + "bio.tool name": "AGAT", + "bio.tool description": "Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.", + "EDAM operation": [ + "Data handling", + "Genome annotation" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/NBISweden/AGAT", + "ToolShed categories": [ + "Convert Formats", + "Statistics", + "Fasta Manipulation" + ], + "ToolShed id": "agat", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", + "Galaxy wrapper version": "1.2.0", + "Conda id": "agat", + "Conda version": "1.4.0", + "EDAM operation (no superclasses)": [ + "Data handling", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "antismash", + "Galaxy tool ids": [ + "antismash" + ], + "Description": "Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters", + "bio.tool id": "antismash", + "bio.tool ids": [ + "antismash" + ], + "biii": null, + "bio.tool name": "antiSMASH", + "bio.tool description": "Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.", + "EDAM operation": [ + "Sequence clustering", + "Gene prediction", + "Differential gene expression analysis" + ], + "EDAM topic": [ + "Molecular interactions, pathways and networks", + "Gene and protein families" + ], + "Status": "To update", + "Source": "https://antismash.secondarymetabolites.org", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "antismash", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/antismash", + "Galaxy wrapper version": "6.1.1", + "Conda id": "antismash", + "Conda version": "7.1.0", + "EDAM operation (no superclasses)": [ + "Sequence clustering", + "Gene prediction", + "Differential gene expression analysis" + ], + "EDAM topic (no superclasses)": [ + "Molecular interactions, pathways and networks", + "Gene and protein families" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on GASLINI": 0, + "Tools available on Galaxy@AuBi": 0, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "atactk_trim_adapters", + "Galaxy tool ids": [ + "atactk_trim_adapters" + ], + "Description": "Trim adapters from paired-end HTS reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ParkerLab/atactk/", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "atactk_trim_adapters", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters", + "Galaxy wrapper version": "0.1.6", + "Conda id": "atactk", + "Conda version": "0.1.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "augustus", + "Galaxy tool ids": [ + "augustus" + ], + "Description": "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bioinf.uni-greifswald.de/augustus/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "augustus", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/augustus", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/augustus", + "Galaxy wrapper version": "3.1.0", + "Conda id": "augustus", + "Conda version": "3.5.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "bamhash", + "Galaxy tool ids": [ + "bamhash" + ], + "Description": "Hash BAM and FASTQ files to verify data integrity", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/DecodeGenetics/BamHash", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bamhash", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bamhash", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bamhash", + "Galaxy wrapper version": "1.1", + "Conda id": "bamhash", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "barcode_collapse", + "Galaxy tool ids": [ + "barcode_collapse" + ], + "Description": "Paired End randomer aware duplicate removal algorithm", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/YeoLab/gscripts", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "barcode_collapse", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse", + "Galaxy wrapper version": "0.1.0", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "bigwig_to_bedgraph", + "Galaxy tool ids": [ + "bigwig_to_bedgraph" + ], + "Description": "Convert from bigWig to bedGraph format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "bigwig_to_bedgraph", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph", + "Galaxy wrapper version": "0.1.0", + "Conda id": "ucsc_tools", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "biomodelsML", + "Galaxy tool ids": [ + "biomodels_biomd0000001066", + "biomodels_biomd0000001076" + ], + "Description": "Wrappers for tools to bring BioModels AI models into Galaxy.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ebi.ac.uk/biomodels/", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "biomodels", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML", + "Galaxy wrapper version": "1.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 2, + "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": "bionano", + "Galaxy tool ids": [ + "bionano_scaffold" + ], + "Description": "Bionano Solve is a set of tools for analyzing Bionano data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bionanogenomics.com/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "bionano", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bionano", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bionano", + "Galaxy wrapper version": "3.7.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "bismark", + "Galaxy tool ids": [ + "bismark_pretty_report", + "bismark_bowtie2", + "bismark_deduplicate", + "bismark_methylation_extractor" + ], + "Description": "A tool to map bisulfite converted sequence reads and determine cytosine methylation states", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.bioinformatics.babraham.ac.uk/projects/bismark/", + "ToolShed categories": [ + "Sequence Analysis", + "Next Gen Mappers" + ], + "ToolShed id": "bismark", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/bismark", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bismark", + "Galaxy wrapper version": "0.22.1", + "Conda id": "bismark", + "Conda version": "0.24.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.fr": 4, + "Tools available on UseGalaxy.org (Main)": 0, + "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": 4, + "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": 4, + "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": 4, + "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": 4, + "Tools available on UseGalaxy.cz": 4, + "Tools available on UseGalaxy.no": 4 + }, + { + "Galaxy wrapper id": "blobtoolkit", + "Galaxy tool ids": [ + "blobtoolkit" + ], + "Description": "Identification and isolation non-target data in draft and publicly available genome assemblies.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://blobtoolkit.genomehubs.org/", + "ToolShed categories": [ + "Sequence Analysis", + "Assembly" + ], + "ToolShed id": "blobtoolkit", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit", + "Galaxy wrapper version": "4.0.7", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "blockbuster", + "Galaxy tool ids": [ + "blockbuster" + ], + "Description": "Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "blockbuster", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster", + "Galaxy wrapper version": "0.1.2", + "Conda id": "blockbuster", + "Conda version": "0.0.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "canu", + "Galaxy tool ids": [ + "canu" + ], + "Description": "Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).", + "bio.tool id": "canu", + "bio.tool ids": [ + "canu" + ], + "biii": null, + "bio.tool name": "CANU", + "bio.tool description": "De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.", + "EDAM operation": [ + "De-novo assembly" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/canu", + "ToolShed categories": [], + "ToolShed id": "canu", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/canu", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/canu", + "Galaxy wrapper version": "2.2", + "Conda id": "canu", + "Conda version": "2.2", + "EDAM operation (no superclasses)": [ + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cellpose", + "Galaxy tool ids": [ + "cellpose" + ], + "Description": "Cellpose is an anatomical segmentation algorithm", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/MouseLand/cellpose", + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "cellpose", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/cellpose", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellpose", + "Galaxy wrapper version": "3.0.8", + "Conda id": "cellpose", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "cellprofiler", + "Galaxy tool ids": [ + "cp_cellprofiler", + "cp_color_to_gray", + "cp_convert_objects_to_image", + "cp_display_data_on_image", + "cp_enhance_or_suppress_features", + "cp_export_to_spreadsheet", + "cp_gray_to_color", + "cp_identify_primary_objects", + "cp_image_math", + "cp_mask_image", + "cp_measure_granularity", + "cp_measure_image_area_occupied", + "cp_measure_image_intensity", + "cp_measure_image_quality", + "cp_measure_object_intensity", + "cp_measure_object_size_shape", + "cp_measure_texture", + "cp_overlay_outlines", + "cp_relate_objects", + "cp_save_images", + "cp_common", + "cp_tile", + "cp_track_objects" + ], + "Description": "cellProfiler wrapper", + "bio.tool id": "CellProfiler", + "bio.tool ids": [ + "CellProfiler" + ], + "biii": "cellprofiler", + "bio.tool name": "CellProfiler", + "bio.tool description": "Tool for quantifying data from biological images, particularly in high-throughput experiments.", + "EDAM operation": [ + "Quantification", + "Image analysis", + "Parsing" + ], + "EDAM topic": [ + "Imaging", + "Microarray experiment", + "Genotype and phenotype" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "cellprofiler", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Quantification", + "Image analysis", + "Parsing" + ], + "EDAM topic (no superclasses)": [ + "Imaging", + "Microarray experiment", + "Genotype and phenotype" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 23, + "Available on UseGalaxy.eu": 23, + "Available on UseGalaxy.fr": 19, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 23, + "Tools available on UseGalaxy.eu": 23, + "Tools available on UseGalaxy.fr": 19, + "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": 19, + "Tools available on UseGalaxy.cz": 23, + "Tools available on UseGalaxy.no": 19 + }, + { + "Galaxy wrapper id": "cellprofiler_v4", + "Galaxy tool ids": [ + "cp_cellprofiler4" + ], + "Description": "cellProfiler4 wrapper", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "cellprofiler4", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4", + "Galaxy wrapper version": "4.2.6", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "chipseeker", + "Galaxy tool ids": [ + "chipseeker" + ], + "Description": "A tool for ChIP peak annotation and visualization", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html", + "ToolShed categories": [ + "ChIP-seq", + "Genome annotation" + ], + "ToolShed id": "chipseeker", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker", + "Galaxy wrapper version": "1.32.0", + "Conda id": "bioconductor-chipseeker", + "Conda version": "1.38.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "circexplorer", + "Galaxy tool ids": [ + "circexplorer" + ], + "Description": "A combined strategy to identify circular RNAs (circRNAs and ciRNAs)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/YangLab/CIRCexplorer", + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "circexplorer", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer", + "Galaxy wrapper version": "1.1.9.0", + "Conda id": "circexplorer", + "Conda version": "1.1.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "combine_metaphlan_humann", + "Galaxy tool ids": [ + "combine_metaphlan_humann" + ], + "Description": "Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances", + "bio.tool id": "combine_metaphlan_and_humann", + "bio.tool ids": [ + "combine_metaphlan_and_humann" + ], + "biii": null, + "bio.tool name": "Combine Metaphlan and HUMAnN", + "bio.tool description": "This tool combine MetaPhlAn outputs and HUMANnN outputs", + "EDAM operation": [ + "Aggregation" + ], + "EDAM topic": [ + "Metagenomics", + "Molecular interactions, pathways and networks" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "combine_metaphlan2_humann2", + "Galaxy wrapper owner": "bebatut", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann", + "Galaxy wrapper version": "0.3.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Aggregation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Molecular interactions, pathways and networks" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "compare_humann2_output", + "Galaxy tool ids": [ + "compare_humann2_output" + ], + "Description": "Compare outputs of HUMAnN2 for several samples and extract similar and specific information", + "bio.tool id": "compare_humann2_outputs", + "bio.tool ids": [ + "compare_humann2_outputs" + ], + "biii": null, + "bio.tool name": "Compare HUMAnN2 outputs", + "bio.tool description": "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples", + "EDAM operation": [ + "Comparison" + ], + "EDAM topic": [ + "Metagenomics", + "Gene and protein families" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "compare_humann2_output", + "Galaxy wrapper owner": "bebatut", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output", + "Galaxy wrapper version": "0.2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Comparison" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Gene and protein families" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cpat", + "Galaxy tool ids": [ + "cpat" + ], + "Description": "Coding-potential assessment tool using an alignment-free logistic regression model.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/liguowang/cpat", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cpat", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/cpat", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/cpat", + "Galaxy wrapper version": "3.0.5", + "Conda id": "cpat", + "Conda version": "3.0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "crt", + "Galaxy tool ids": [ + "crispr_recognition_tool" + ], + "Description": "CRISPR Recognition Tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "crispr_recognition_tool", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/crt", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/crt", + "Galaxy wrapper version": "1.2.0", + "Conda id": "crisper_recognition_tool", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "diff", + "Galaxy tool ids": [ + "diff" + ], + "Description": "GNU diff tool that calculates the differences between two files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.gnu.org/software/diffutils/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "diff", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/diff", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/diff", + "Galaxy wrapper version": "3.7", + "Conda id": "diffutils", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "diffbind", + "Galaxy tool ids": [], + "Description": "Diffbind provides functions for processing ChIP-Seq data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bioconductor.org/packages/release/bioc/html/DiffBind.html", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "diffbind", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/diffbind", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/diffbind", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "ear", + "Galaxy tool ids": [ + "make_ear" + ], + "Description": "A tool to compile assembly reports and stastics from assembly pipeline", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ERGA-consortium/EARs/tree/main", + "ToolShed categories": [ + "Sequence Analysis", + "Assembly" + ], + "ToolShed id": "erga_ear", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/ERGA-consortium/EARs/tree/main", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/ear", + "Galaxy wrapper version": "1.0.0", + "Conda id": "reportlab", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "edta", + "Galaxy tool ids": [ + "edta" + ], + "Description": "The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. ", + "bio.tool id": "edta", + "bio.tool ids": [ + "edta" + ], + "biii": null, + "bio.tool name": "The Extensive de novo TE Annotator (EDTA)", + "bio.tool description": "The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.", + "EDAM operation": [ + "De-novo assembly", + "Deisotoping", + "Genome annotation" + ], + "EDAM topic": [ + "Workflows", + "Mobile genetic elements", + "Plant biology", + "Transcription factors and regulatory sites", + "Model organisms" + ], + "Status": "To update", + "Source": "https://github.com/oushujun/EDTA", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "edta", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/edta", + "Galaxy wrapper version": null, + "Conda id": "edta", + "Conda version": "2.2.0", + "EDAM operation (no superclasses)": [ + "De-novo assembly", + "Deisotoping", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Workflows", + "Mobile genetic elements", + "Plant biology", + "Transcription factors and regulatory sites", + "Model organisms" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "epicseg", + "Galaxy tool ids": [ + "epicseg_segment" + ], + "Description": "EpiCSeg is a tool for conducting chromatin segmentation.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/lamortenera/epicseg", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "epicseg", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/epicseg", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/epicseg", + "Galaxy wrapper version": "@VERSION_STRING@", + "Conda id": "epicseg", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "fastq_info", + "Galaxy tool ids": [ + "fastq_info" + ], + "Description": "FASTQ info allows to validate single or paired fastq files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nunofonseca/fastq_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_info", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info", + "Galaxy wrapper version": "0.25.1", + "Conda id": "fastq_utils", + "Conda version": "0.25.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "file_manipulation", + "Galaxy tool ids": [ + "bg_uniq" + ], + "Description": "This tool returns all unique lines from a tab-separated file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "unique", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation", + "Galaxy wrapper version": "0.4", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "find_subsequences", + "Galaxy tool ids": [ + "bg_find_subsequences" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "find_subsequences", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences", + "Galaxy wrapper version": "0.3", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "flye", + "Galaxy tool ids": [ + "flye" + ], + "Description": "Assembly of long and error-prone reads.", + "bio.tool id": "Flye", + "bio.tool ids": [ + "Flye" + ], + "biii": null, + "bio.tool name": "Flye", + "bio.tool description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.", + "EDAM operation": [ + "Genome assembly", + "De-novo assembly", + "Mapping assembly", + "Cross-assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Metagenomics", + "Whole genome sequencing", + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/fenderglass/Flye/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "flye", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/flye", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/flye", + "Galaxy wrapper version": "2.9.3", + "Conda id": "flye", + "Conda version": "2.9.4", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "De-novo assembly", + "Mapping assembly", + "Cross-assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Metagenomics", + "Whole genome sequencing" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "footprint", + "Galaxy tool ids": [ + "footprint" + ], + "Description": "Find transcription factor footprints", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "footprint", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/footprint", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/footprint", + "Galaxy wrapper version": "1.0.0", + "Conda id": "footprint", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "format_cd_hit_output", + "Galaxy tool ids": [ + "format_cd_hit_output" + ], + "Description": "Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "format_cd_hit_output", + "Galaxy wrapper owner": "bebatut", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output", + "Galaxy wrapper version": "1.0.0+galaxy1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "format_metaphlan2_output", + "Galaxy tool ids": [ + "format_metaphlan2_output" + ], + "Description": "Format MetaPhlAn2 output to extract abundance at different taxonomic levels", + "bio.tool id": "format_metaphlan2_output", + "bio.tool ids": [ + "format_metaphlan2_output" + ], + "biii": null, + "bio.tool name": "Format metaphlan2 output", + "bio.tool description": "This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).", + "EDAM operation": [ + "Formatting" + ], + "EDAM topic": [ + "Taxonomy", + "Metagenomics" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "format_metaphlan2_output", + "Galaxy wrapper owner": "bebatut", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output", + "Galaxy wrapper version": "0.2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Formatting" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy", + "Metagenomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "gfastats", + "Galaxy tool ids": [ + "gfastats" + ], + "Description": "Tool for generating sequence statistics and simultaneous genome assembly file manipulation.", + "bio.tool id": "gfastats", + "bio.tool ids": [ + "gfastats" + ], + "biii": null, + "bio.tool name": "gfastats", + "bio.tool description": "gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.", + "EDAM operation": [ + "Data handling" + ], + "EDAM topic": [ + "Computational biology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/vgl-hub/gfastats", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gfastats", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/gfastats", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/gfastats", + "Galaxy wrapper version": "1.3.6", + "Conda id": "gfastats", + "Conda version": "1.3.6", + "EDAM operation (no superclasses)": [ + "Data handling" + ], + "EDAM topic (no superclasses)": [ + "Computational biology" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "glimmer_hmm", + "Galaxy tool ids": [], + "Description": "GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://ccb.jhu.edu/software/glimmerhmm/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "glimmer_hmm", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "gotohscan", + "Galaxy tool ids": [ + "rbc_gotohscan" + ], + "Description": "Find subsequences in db", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gotohscan", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan", + "Galaxy wrapper version": "1.3.0", + "Conda id": "gotohscan", + "Conda version": "1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "graph_converter", + "Galaxy tool ids": [ + "graph_converter" + ], + "Description": "Convert between different graph formats", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "graph_converter", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter", + "Galaxy wrapper version": "0.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "graphclust", + "Galaxy tool ids": [ + "graphclust" + ], + "Description": "GraphClust can be used for structural clustering of RNA sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.bioinf.uni-freiburg.de/Software/GraphClust/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "graphclust", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graphclust", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graphclust", + "Galaxy wrapper version": "0.1", + "Conda id": "GraphClust", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "graphmap", + "Galaxy tool ids": [ + "graphmap_align", + "graphmap_overlap" + ], + "Description": "Mapper for long, error-prone reads.", + "bio.tool id": "graphmap", + "bio.tool ids": [ + "graphmap" + ], + "biii": null, + "bio.tool name": "graphmap", + "bio.tool description": "Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1", + "EDAM operation": [ + "Sequence trimming", + "EST assembly", + "Read mapping" + ], + "EDAM topic": [ + "Gene transcripts", + "RNA-Seq", + "RNA splicing" + ], + "Status": "To update", + "Source": "https://github.com/isovic/graphmap/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "graphmap", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/graphmap", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graphmap", + "Galaxy wrapper version": "0.5.2", + "Conda id": "graphmap", + "Conda version": "0.6.3", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "EST assembly", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Gene transcripts", + "RNA-Seq", + "RNA splicing" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 2, + "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": 2, + "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": 2, + "Tools available on UseGalaxy.cz": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "hclust2", + "Galaxy tool ids": [ + "hclust2" + ], + "Description": "Plots heatmaps", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/nsegata/hclust2/", + "ToolShed categories": [ + "Data Visualization" + ], + "ToolShed id": "hclust2", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hclust2", + "Galaxy wrapper version": "0.99", + "Conda id": "hclust2", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "hictk", + "Galaxy tool ids": [ + "hictk" + ], + "Description": "Convert cooler to juicebox_hic", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/paulsengroup/hictk", + "ToolShed categories": [ + "Convert Formats", + "Epigenetics" + ], + "ToolShed id": "hictk", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hictk", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hictk", + "Galaxy wrapper version": "0.0.12", + "Conda id": "hictk", + "Conda version": "0.0.12", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "hicup", + "Galaxy tool ids": [ + "hicup2juicer", + "hicup_deduplicator", + "hicup_digester", + "hicup_filter", + "hicup_hicup", + "hicup_mapper", + "hicup_truncater" + ], + "Description": "The HiCUP-Pipeline from the Bioinformatics Babraham Institute.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "hicup", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hicup", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hicup", + "Galaxy wrapper version": "0.9.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 7, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 7, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 7, + "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": 7, + "Tools available on UseGalaxy.no": 6 + }, + { + "Galaxy wrapper id": "hifiasm", + "Galaxy tool ids": [ + "hifiasm" + ], + "Description": "A fast haplotype-resolved de novo assembler", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/chhylp123/hifiasm", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hifiasm", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm", + "Galaxy wrapper version": "0.19.8", + "Conda id": "hifiasm", + "Conda version": "0.19.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "homer", + "Galaxy tool ids": [], + "Description": "Software for motif discovery and next generation sequencing analysis.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://homer.salk.edu/homer/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "homer", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/homer", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/homer", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "illumina_methylation_analyser", + "Galaxy tool ids": [ + "illumina_methylation_analyser" + ], + "Description": "Methylation analyzer for Illumina 450k DNA emthylation microarrays", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "illumina_methylation_analyser", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser", + "Galaxy wrapper version": "0.1", + "Conda id": "Rscript", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "bia-ftplinks", + "Galaxy tool ids": [ + "bia_download" + ], + "Description": "Tool to query ftp links for study from bioimage archive", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "bia_download", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks", + "Galaxy wrapper version": "0.1.0", + "Conda id": "wget", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "graphicsmagick", + "Galaxy tool ids": [ + "graphicsmagick_image_compare", + "graphicsmagick_image_convert", + "graphicsmagick_image_montage" + ], + "Description": "Contains tools based on GraphicsMagick", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.graphicsmagick.org", + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "graphicsmagick", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick", + "Galaxy wrapper version": "1.3.43", + "Conda id": "graphicsmagick", + "Conda version": "1.3.26", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 3, + "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": 2, + "Tools available on UseGalaxy.cz": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "imagej2", + "Galaxy tool ids": [ + "imagej2_adjust_threshold_binary", + "imagej2_analyze_particles_binary", + "imagej2_analyze_skeleton", + "imagej2_binary_to_edm", + "imagej2_bunwarpj_adapt_transform", + "imagej2_bunwarpj_align", + "imagej2_bunwarpj_compare_elastic", + "imagej2_bunwarpj_compare_elastic_raw", + "imagej2_bunwarpj_compare_raw", + "imagej2_bunwarpj_compose_elastic", + "imagej2_bunwarpj_compose_raw", + "imagej2_bunwarpj_compose_raw_elastic", + "imagej2_bunwarpj_convert_to_raw", + "imagej2_bunwarpj_elastic_transform", + "imagej2_bunwarpj_raw_transform", + "imagej2_create_image", + "imagej2_enhance_contrast", + "imagej2_find_edges", + "imagej2_find_maxima", + "imagej2_make_binary", + "imagej2_math", + "imagej2_noise", + "imagej2_shadows", + "imagej2_sharpen", + "imagej2_skeletonize3d", + "imagej2_smooth", + "imagej2_watershed_binary" + ], + "Description": "ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.", + "bio.tool id": "imagej", + "bio.tool ids": [ + "imagej" + ], + "biii": "imagej2", + "bio.tool name": "ImageJ2", + "bio.tool description": "It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.", + "EDAM operation": [ + "Image analysis", + "Image annotation", + "Visualisation" + ], + "EDAM topic": [ + "Imaging" + ], + "Status": "To update", + "Source": "http://fiji.sc", + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "imagej2", + "Galaxy wrapper owner": "imgteam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Image analysis", + "Image annotation", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Imaging" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 27, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 27, + "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": 27, + "Tools available on UseGalaxy.no": 27 + }, + { + "Galaxy wrapper id": "woundhealing", + "Galaxy tool ids": [ + "woundhealing_scratch_assay" + ], + "Description": "Tool to automate quantification of wound healing in high-throughput microscopy scratch assays", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://git.embl.de/grp-cba/wound-healing-htm-screen", + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "Wound healing scratch assay image analysis", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing", + "Galaxy wrapper version": "1.6.1", + "Conda id": "fiji-morpholibj", + "Conda version": "1.6.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "instagraal", + "Galaxy tool ids": [ + "instagraal" + ], + "Description": "Large genome reassembly based on Hi-C data", + "bio.tool id": "instagraal", + "bio.tool ids": [ + "instagraal" + ], + "biii": null, + "bio.tool name": "instaGRAAL", + "bio.tool description": "Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)", + "EDAM operation": [ + "Genome assembly", + "Mapping assembly", + "Genetic mapping", + "Scaffolding" + ], + "EDAM topic": [ + "Sequence assembly", + "Mapping", + "Metagenomics", + "Statistics and probability", + "DNA binding sites" + ], + "Status": "To update", + "Source": "https://github.com/koszullab/instaGRAAL", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "instagraal", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/instagraal", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/instagraal", + "Galaxy wrapper version": "0.1.6", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Mapping assembly", + "Genetic mapping", + "Scaffolding" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Mapping", + "Metagenomics", + "Statistics and probability", + "DNA binding sites" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "iprscan5", + "Galaxy tool ids": [], + "Description": "Interproscan queries the interpro database and provides annotations.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.ebi.ac.uk/Tools/pfa/iprscan5/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "iprscan5", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "itsx", + "Galaxy tool ids": [ + "itsx" + ], + "Description": "ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.", + "bio.tool id": "ITSx", + "bio.tool ids": [ + "ITSx" + ], + "biii": null, + "bio.tool name": "ITSx", + "bio.tool description": "TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.", + "EDAM operation": [ + "Sequence feature detection" + ], + "EDAM topic": [ + "Functional, regulatory and non-coding RNA", + "Microbiology" + ], + "Status": "Up-to-date", + "Source": "https://microbiology.se/software/itsx/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "itsx", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/itsx", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/itsx", + "Galaxy wrapper version": "1.1.3", + "Conda id": "itsx", + "Conda version": "1.1.3", + "EDAM operation (no superclasses)": [ + "Sequence feature detection" + ], + "EDAM topic (no superclasses)": [ + "Functional, regulatory and non-coding RNA", + "Microbiology" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "jbrowse2", + "Galaxy tool ids": [ + "jbrowse2" + ], + "Description": "JBrowse2 Genome Browser integrated as a Galaxy Tool", + "bio.tool id": "jbrowse2", + "bio.tool ids": [ + "jbrowse2" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://jbrowse.org", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "jbrowse2", + "Galaxy wrapper owner": "fubar", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2", + "Galaxy wrapper version": "2.11.1", + "Conda id": "jbrowse2", + "Conda version": "2.11.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "jupyter_job", + "Galaxy tool ids": [ + "run_jupyter_job" + ], + "Description": "Run jupyter notebook script in Galaxy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "run_jupyter_job", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job", + "Galaxy wrapper version": "0.0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "labels", + "Galaxy tool ids": [ + "bg_labels" + ], + "Description": "remaps and annotates alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "labels", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/labels", + "Galaxy wrapper version": "1.0.5.0", + "Conda id": "labels", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "lighter", + "Galaxy tool ids": [ + "lighter" + ], + "Description": "Lighter is a kmer-based error correction method for whole genome sequencing data", + "bio.tool id": "lighter", + "bio.tool ids": [ + "lighter" + ], + "biii": null, + "bio.tool name": "Lighter", + "bio.tool description": "Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.", + "EDAM operation": [ + "k-mer counting", + "Sequence read processing", + "Sequencing quality control", + "Sequencing error detection" + ], + "EDAM topic": [ + "Sequencing", + "Whole genome sequencing", + "DNA", + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/mourisl/Lighter", + "ToolShed categories": [ + "Sequence Analysis", + "Fasta Manipulation" + ], + "ToolShed id": "lighter", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/lighter", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/lighter", + "Galaxy wrapper version": "1.0", + "Conda id": "lighter", + "Conda version": "1.1.3", + "EDAM operation (no superclasses)": [ + "k-mer counting", + "Sequence read processing", + "Sequencing quality control", + "Sequencing error detection" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "DNA", + "Genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "mafft", + "Galaxy tool ids": [ + "rbc_mafft_add", + "rbc_mafft" + ], + "Description": "Multiple alignment program for amino acid or nucleotide sequences", + "bio.tool id": "MAFFT", + "bio.tool ids": [ + "MAFFT" + ], + "biii": null, + "bio.tool name": "MAFFT", + "bio.tool description": "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.", + "EDAM operation": [ + "Multiple sequence alignment" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://mafft.cbrc.jp/alignment/software/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "mafft", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mafft", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mafft", + "Galaxy wrapper version": "7.520", + "Conda id": "mafft", + "Conda version": "7.525", + "EDAM operation (no superclasses)": [ + "Multiple sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 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": 1, + "Tools available on BioBix": 0, + "Tools available on CIRM-CFBP": 0, + "Tools available on Center for Phage Technology (CPT)": 2, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 2, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 2, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 2, + "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": 2, + "Tools available on UseGalaxy.cz": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "mavedb", + "Galaxy tool ids": [ + "mavedb_importer" + ], + "Description": "data source for MaveDB", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "mavedb_importer", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb", + "Galaxy wrapper version": "0.9", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "methtools", + "Galaxy tool ids": [ + "methtools_calling", + "r_correlation_matrix", + "methtools_destrand", + "methtools_dmr", + "methtools_filter", + "methtools_plot", + "smooth_running_window", + "methtools_tiling" + ], + "Description": "tools for methylation analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "methtools", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methtools", + "Galaxy wrapper version": "0.1.1", + "Conda id": "methtools", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "methyldackel", + "Galaxy tool ids": [ + "pileometh" + ], + "Description": "A tool for processing bisulfite sequencing alignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/dpryan79/MethylDackel", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pileometh", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel", + "Galaxy wrapper version": "0.5.2", + "Conda id": "methyldackel", + "Conda version": "0.6.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "methylkit", + "Galaxy tool ids": [ + "methylkit" + ], + "Description": "A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bioconductor.org/packages/release/bioc/html/methylKit.html", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "methylkit", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/methylkit", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/methylkit", + "Galaxy wrapper version": "0.99.2", + "Conda id": "bioconductor-methylkit", + "Conda version": "1.28.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "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": "metilene", + "Galaxy tool ids": [ + "metilene" + ], + "Description": "Differential DNA methylation calling", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA", + "Statistics" + ], + "ToolShed id": "metilene", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/metilene", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/metilene", + "Galaxy wrapper version": "0.2.6.1", + "Conda id": "metilene", + "Conda version": "0.2.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "mgnify_seqprep", + "Galaxy tool ids": [ + "mgnify_seqprep" + ], + "Description": "A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.", + "bio.tool id": "seqprep", + "bio.tool ids": [ + "seqprep" + ], + "biii": null, + "bio.tool name": "SeqPrep", + "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", + "EDAM operation": [ + "Nucleic acid design" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly", + "Sequencing", + "Probes and primers" + ], + "Status": "To update", + "Source": "https://github.com/jstjohn/SeqPrep", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "mgnify_seqprep", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep", + "Galaxy wrapper version": "1.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Nucleic acid design" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly", + "Sequencing", + "Probes and primers" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "miclip", + "Galaxy tool ids": [ + "mi_clip" + ], + "Description": "Identification of binding sites in CLIP-Seq data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cran.r-project.org/src/contrib/Archive/MiClip/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "miclip", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/miclip", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/miclip", + "Galaxy wrapper version": "1.2.0", + "Conda id": "Rscript", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "minced", + "Galaxy tool ids": [ + "minced" + ], + "Description": "MinCED - Mining CRISPRs in Environmental Datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "minced", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/minced", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/minced", + "Galaxy wrapper version": "0.2.0", + "Conda id": "minced", + "Conda version": "0.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "minipolish", + "Galaxy tool ids": [ + "minipolish" + ], + "Description": "Polishing miniasm assemblies", + "bio.tool id": "minipolish", + "bio.tool ids": [ + "minipolish" + ], + "biii": null, + "bio.tool name": "minipolish", + "bio.tool description": "A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.", + "EDAM operation": [ + "Localised reassembly", + "Read depth analysis" + ], + "EDAM topic": [ + "Sequence assembly", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/rrwick/Minipolish", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "minipolish", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/minipolish", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/minipolish", + "Galaxy wrapper version": "0.1.3", + "Conda id": "minipolish", + "Conda version": "0.1.3", + "EDAM operation (no superclasses)": [ + "Localised reassembly", + "Read depth analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Sequencing" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "mitohifi", + "Galaxy tool ids": [ + "mitohifi" + ], + "Description": "Assembly mitogenomes from Pacbio HiFi read.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "mitohifi", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi", + "Galaxy wrapper version": "3", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "molecule2gspan", + "Galaxy tool ids": [ + "bg_mol2gspan" + ], + "Description": "converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "molecule_to_gspan", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan", + "Galaxy wrapper version": "0.2", + "Conda id": "openbabel", + "Conda version": "2.3.90dev7d621d9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "music_deconvolution", + "Galaxy tool ids": [ + "music_construct_eset", + "music_inspect_eset", + "music_manipulate_eset", + "music_compare", + "music_deconvolution" + ], + "Description": "Multi-subject Single Cell deconvolution (MuSiC)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/xuranw/MuSiC", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "music", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution", + "Galaxy wrapper version": "0.1.1", + "Conda id": "music-deconvolution", + "Conda version": "0.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 5, + "Tools available on UseGalaxy.org.au": 5, + "Tools available on UseGalaxy.eu": 4, + "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": 5, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "nanopolish", + "Galaxy tool ids": [ + "nanopolish_eventalign", + "nanopolish_methylation", + "nanopolish_polya", + "nanopolish_variants" + ], + "Description": "Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/jts/nanopolish", + "ToolShed categories": [], + "ToolShed id": "nanopolish", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish", + "Galaxy wrapper version": "0.14.0", + "Conda id": "nanopolish", + "Conda version": "0.14.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.fr": 4, + "Tools available on UseGalaxy.org (Main)": 0, + "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)": 3, + "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": 2, + "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": 4, + "Tools available on UseGalaxy.cz": 4, + "Tools available on UseGalaxy.no": 4 + }, + { + "Galaxy wrapper id": "netboxr", + "Galaxy tool ids": [ + "netboxr" + ], + "Description": "netboxr enables automated discovery of biological process modules by network analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Systems Biology" + ], + "ToolShed id": "netboxr", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/netboxr", + "Galaxy wrapper version": "1.6.0", + "Conda id": "bioconductor-netboxr", + "Conda version": "1.9.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "nextdenovo", + "Galaxy tool ids": [ + "nextdenovo" + ], + "Description": "String graph-based de novo assembler for long reads", + "bio.tool id": "nextdenovo", + "bio.tool ids": [ + "nextdenovo" + ], + "biii": null, + "bio.tool name": "NextDenovo", + "bio.tool description": "NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a \"correct-then-assemble\" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.", + "EDAM operation": [ + "De-novo assembly", + "Genome assembly" + ], + "EDAM topic": [ + "Sequencing", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/Nextomics/NextDenovo", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "nextdenovo", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo", + "Galaxy wrapper version": "2.5.0", + "Conda id": "nextdenovo", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "De-novo assembly", + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "nucleosome_prediction", + "Galaxy tool ids": [ + "Nucleosome" + ], + "Description": "Prediction of Nucleosomes Positions on the Genome", + "bio.tool id": "nucleosome_prediction", + "bio.tool ids": [ + "nucleosome_prediction" + ], + "biii": null, + "bio.tool name": "nucleosome_prediction", + "bio.tool description": "Prediction of Nucleosomes Positions on the Genome", + "EDAM operation": [ + "Prediction and recognition", + "Nucleosome position prediction", + "Sequence analysis" + ], + "EDAM topic": [ + "Structural genomics", + "Nucleic acid sites, features and motifs" + ], + "Status": "Up-to-date", + "Source": "https://genie.weizmann.ac.il/software/nucleo_exe.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "nucleosome_prediction", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction", + "Galaxy wrapper version": "3.0", + "Conda id": "nucleosome_prediction", + "Conda version": "3.0", + "EDAM operation (no superclasses)": [ + "Prediction and recognition", + "Nucleosome position prediction", + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Structural genomics", + "Nucleic acid sites, features and motifs" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "numeric_clustering", + "Galaxy tool ids": [ + "numeric_clustering" + ], + "Description": "Clustering tool for numberic values", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://scikit-learn.org/stable/index.html", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "numeric_clustering", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering", + "Galaxy wrapper version": "0.9", + "Conda id": "anaconda", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": "openms", + "Galaxy tool ids": [ + "AccurateMassSearch", + "AdditiveSeries", + "BaselineFilter", + "CVInspector", + "CompNovo", + "CompNovoCID", + "ConsensusID", + "ConsensusMapNormalizer", + "ConvertTSVToTraML", + "ConvertTraMLToTSV", + "DTAExtractor", + "DeMeanderize", + "Decharger", + "DecoyDatabase", + "Digestor", + "DigestorMotif", + "EICExtractor", + "ERPairFinder", + "ExternalCalibration", + "FFEval", + "FalseDiscoveryRate", + "FeatureFinderCentroided", + "FeatureFinderIdentification", + "FeatureFinderIsotopeWavelet", + "FeatureFinderMRM", + "FeatureFinderMetabo", + "FeatureFinderMultiplex", + "FeatureFinderSuperHirn", + "FeatureLinkerLabeled", + "FeatureLinkerUnlabeled", + "FeatureLinkerUnlabeledQT", + "FidoAdapter", + "FileConverter", + "FileFilter", + "FileInfo", + "FileMerger", + "FuzzyDiff", + "HighResPrecursorMassCorrector", + "IDConflictResolver", + "IDDecoyProbability", + "IDExtractor", + "IDFileConverter", + "IDFilter", + "IDMapper", + "IDMassAccuracy", + "IDMerger", + "IDPosteriorErrorProbability", + "IDRTCalibration", + "IDRipper", + "IDScoreSwitcher", + "IDSplitter", + "ITRAQAnalyzer", + "InclusionExclusionListCreator", + "InspectAdapter", + "InternalCalibration", + "IsobaricAnalyzer", + "LabeledEval", + "LowMemPeakPickerHiRes", + "LowMemPeakPickerHiRes_RandomAccess", + "LuciphorAdapter", + "MRMMapper", + "MRMPairFinder", + "MRMTransitionGroupPicker", + "MSGFPlusAdapter", + "MSSimulator", + "MapAlignmentEvaluation", + "MapNormalizer", + "MapRTTransformer", + "MapStatistics", + "MascotAdapter", + "MascotAdapterOnline", + "MassCalculator", + "MassTraceExtractor", + "MetaProSIP", + "MetaboliteSpectralMatcher", + "MultiplexResolver", + "MzMLSplitter", + "MzTabExporter", + "NoiseFilterGaussian", + "NoiseFilterSGolay", + "OpenSwathAnalyzer", + "OpenSwathAssayGenerator", + "OpenSwathChromatogramExtractor", + "OpenSwathConfidenceScoring", + "OpenSwathDIAPreScoring", + "OpenSwathDecoyGenerator", + "OpenSwathFeatureXMLToTSV", + "OpenSwathFileSplitter", + "OpenSwathMzMLFileCacher", + "OpenSwathRTNormalizer", + "OpenSwathRewriteToFeatureXML", + "OpenSwathWorkflow", + "PTModel", + "PTPredict", + "PeakPickerHiRes", + "PeakPickerIterative", + "PeakPickerWavelet", + "PepNovoAdapter", + "PeptideIndexer", + "PhosphoScoring", + "PrecursorIonSelector", + "PrecursorMassCorrector", + "ProteinInference", + "ProteinQuantifier", + "ProteinResolver", + "QCCalculator", + "QCEmbedder", + "QCExporter", + "QCExtractor", + "QCImporter", + "QCMerger", + "QCShrinker", + "RNPxl", + "RNPxlXICFilter", + "RTEvaluation", + "RTModel", + "RTPredict", + "SemanticValidator", + "SequenceCoverageCalculator", + "SimpleSearchEngine", + "SpecLibCreator", + "SpectraFilterBernNorm", + "SpectraFilterMarkerMower", + "SpectraFilterNLargest", + "SpectraFilterNormalizer", + "SpectraFilterParentPeakMower", + "SpectraFilterScaler", + "SpectraFilterSqrtMower", + "SpectraFilterThresholdMower", + "SpectraFilterWindowMower", + "SpectraMerger", + "SvmTheoreticalSpectrumGeneratorTrainer", + "TICCalculator", + "TMTAnalyzer", + "TOFCalibration", + "TextExporter", + "TopPerc", + "TransformationEvaluation", + "XMLValidator", + "XTandemAdapter" + ], + "Description": "OpenMS in version 2.1.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "openms", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/openms", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/openms", + "Galaxy wrapper version": "2.1.0", + "Conda id": "openms", + "Conda version": "3.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 7, + "Available on UseGalaxy.org.au": 34, + "Available on UseGalaxy.eu": 135, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 7, + "Tools available on UseGalaxy.org.au": 34, + "Tools available on UseGalaxy.eu": 135, + "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": 19, + "Tools available on UseGalaxy.cz": 135, + "Tools available on UseGalaxy.no": 134 + }, + { + "Galaxy wrapper id": "pandas_rolling_window", + "Galaxy tool ids": [ + "pandas_rolling_window" + ], + "Description": "Rolling window calculations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "pandas_rolling_window", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window", + "Galaxy wrapper version": "0.1", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "peakachu", + "Galaxy tool ids": [ + "peakachu" + ], + "Description": "PEAKachu is a peak-caller for CLIP- and RIP-Seq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "peakachu", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/tbischler/PEAKachu", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/peakachu", + "Galaxy wrapper version": "0.2.0+galaxy1", + "Conda id": "peakachu", + "Conda version": "0.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "perf", + "Galaxy tool ids": [ + "stats_perf_tool" + ], + "Description": "suitable for boolean classification problems", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://osmot.cs.cornell.edu/kddcup/software.html", + "ToolShed categories": [], + "ToolShed id": "stats_perf_tool", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/perf", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/perf", + "Galaxy wrapper version": "5.11.0", + "Conda id": "perf", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pfamscan", + "Galaxy tool ids": [ + "pfamscan" + ], + "Description": "Search a FASTA sequence against a library of Pfam HMM.", + "bio.tool id": "pfamscan", + "bio.tool ids": [ + "pfamscan" + ], + "biii": null, + "bio.tool name": "PfamScan", + "bio.tool description": "This tool is used to search a FASTA sequence against a library of Pfam HMM.", + "EDAM operation": [ + "Protein sequence analysis" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pfamscan", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan", + "Galaxy wrapper version": "1.6", + "Conda id": "pfam_scan", + "Conda version": "1.6", + "EDAM operation (no superclasses)": [ + "Protein sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "pg_tools", + "Galaxy tool ids": [ + "pg_dump", + "pg_import", + "pg_query" + ], + "Description": "tool suite for dealing with Postgresql databases from Galaxy's history", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.postgresql.org", + "ToolShed categories": [ + "Data Export", + "Data Source" + ], + "ToolShed id": "pgtools", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tools/pgtools", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools", + "Galaxy wrapper version": null, + "Conda id": "postgresql", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "pharmcat", + "Galaxy tool ids": [ + "pharmcat" + ], + "Description": "Pharmacogenomics Clinical Annotation Tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pharmcat.org/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pharmcat", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "piranha", + "Galaxy tool ids": [ + "piranha" + ], + "Description": "Piranha is a peak-caller for CLIP- and RIP-Seq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "piranha", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/piranha", + "Galaxy wrapper version": "1.2.1.0", + "Conda id": "piranha", + "Conda version": "1.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "platypus", + "Galaxy tool ids": [ + "bg_platypus" + ], + "Description": "efficient and accurate variant-detection in high-throughput sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.well.ox.ac.uk/platypus", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "platypus", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/platypus", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/platypus", + "Galaxy wrapper version": "0.0.11", + "Conda id": "platypus", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "plotly_ml_performance_plots", + "Galaxy tool ids": [ + "plotly_ml_performance_plots" + ], + "Description": "performance plots for machine learning problems", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "plotly_ml_performance_plots", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots", + "Galaxy wrapper version": "0.3", + "Conda id": "galaxy-ml", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "plotly_parallel_coordinates_plot", + "Galaxy tool ids": [ + "plotly_parallel_coordinates_plot" + ], + "Description": "parallel coordinates plot produced with plotly", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://plot.ly/python/parallel-coordinates-plot/", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "plotly_parallel_coordinates_plot", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot", + "Galaxy wrapper version": "0.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "plotly_regression_performance_plots", + "Galaxy tool ids": [ + "plotly_regression_performance_plots" + ], + "Description": "performance plots for regression problems", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://scikit-learn.org/stable/supervised_learning.html#supervised-learning", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "plotly_regression_performance_plots", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots", + "Galaxy wrapper version": "0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "protease_prediction", + "Galaxy tool ids": [ + "eden_protease_prediction" + ], + "Description": "This tool can learn the cleavage specificity of a given class of proteases.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/fabriziocosta/eden", + "ToolShed categories": [ + "Sequence Analysis", + "Proteomics" + ], + "ToolShed id": "protease_prediction", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction", + "Galaxy wrapper version": "0.9", + "Conda id": "eden", + "Conda version": "2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "protein_properties", + "Galaxy tool ids": [ + "bg_protein_properties" + ], + "Description": "Calculation of various properties from given protein sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "protein_properties", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties", + "Galaxy wrapper version": "0.2.0", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "improviser", + "Galaxy tool ids": [ + "proteomics_improviser" + ], + "Description": "Visualisation of PepXML files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.improviser.uni-freiburg.de/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomics_improviser", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser", + "Galaxy wrapper version": "1.1.0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "racon", + "Galaxy tool ids": [ + "racon" + ], + "Description": "Consensus module for raw de novo DNA assembly of long uncorrected reads.", + "bio.tool id": "Racon", + "bio.tool ids": [ + "Racon" + ], + "biii": null, + "bio.tool name": "Racon", + "bio.tool description": "Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.", + "EDAM operation": [ + "Genome assembly", + "Mapping assembly" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/isovic/racon", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "racon", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/racon", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/racon", + "Galaxy wrapper version": "1.5.0", + "Conda id": "racon", + "Conda version": "1.5.0", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Mapping assembly" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "repeat_masker", + "Galaxy tool ids": [ + "repeatmasker_wrapper" + ], + "Description": "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.repeatmasker.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "repeat_masker", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker", + "Galaxy wrapper version": "0.1.2", + "Conda id": "RepeatMasker", + "Conda version": "4.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "replaceColumn", + "Galaxy tool ids": [ + "replace_column_with_key_value_file" + ], + "Description": "A tool to replace all column entries of a file given by values of a key-value file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "replace_column_by_key_value_file", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn", + "Galaxy wrapper version": "0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rest_tool", + "Galaxy tool ids": [ + "pubchem_rest_tool" + ], + "Description": "This tool fetches data from pubchem via the PubChem REST API.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "pubchem_rest_tool", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool", + "Galaxy wrapper version": "0.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "antarna", + "Galaxy tool ids": [ + "antarna" + ], + "Description": "antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "antarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna", + "Galaxy wrapper version": "1.1", + "Conda id": "antarna", + "Conda version": "2.0.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "aresite2", + "Galaxy tool ids": [ + "AREsite2_REST" + ], + "Description": "AREsite2 REST Interface", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rna.tbi.univie.ac.at/AREsite", + "ToolShed categories": [ + "RNA", + "Data Source", + "Sequence Analysis" + ], + "ToolShed id": "aresite2", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2", + "Galaxy wrapper version": "0.1.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "blockclust", + "Galaxy tool ids": [ + "blockclust" + ], + "Description": "BlockClust detects transcripts with similar processing patterns.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "blockclust", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust", + "Galaxy wrapper version": "1.1.1", + "Conda id": "blockclust", + "Conda version": "1.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "cmsearch_deoverlap", + "Galaxy tool ids": [ + "cmsearch_deoverlap" + ], + "Description": "removes lower scoring overlaps from cmsearch results.", + "bio.tool id": "cmsearch-deoverlap", + "bio.tool ids": [ + "cmsearch-deoverlap" + ], + "biii": null, + "bio.tool name": "cmsearch-deoverlap", + "bio.tool description": "Removes lower scoring overlaps from cmsearch results.", + "EDAM operation": [ + "Comparison", + "Alignment" + ], + "EDAM topic": [ + "Biology", + "Medicine" + ], + "Status": "To update", + "Source": "https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "cmsearch_deoverlap", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap", + "Galaxy wrapper version": "0.08+galaxy2", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Comparison", + "Alignment" + ], + "EDAM topic (no superclasses)": [ + "Biology", + "Medicine" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "cmv", + "Galaxy tool ids": [ + "cmcv", + "cmv", + "hmmcv", + "hmmv" + ], + "Description": "cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/eggzilla/cmv", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "cmv", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv", + "Galaxy wrapper version": "1.0.8", + "Conda id": "cmv", + "Conda version": "1.0.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 2, + "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": 2, + "Tools available on UseGalaxy.no": 2 + }, + { + "Galaxy wrapper id": "cofold", + "Galaxy tool ids": [ + "cofold" + ], + "Description": "Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.e-rna.org/cofold/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "cofold", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold", + "Galaxy wrapper version": "2.0.4.0", + "Conda id": "cofold", + "Conda version": "2.0.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "compalignp", + "Galaxy tool ids": [ + "compalignp" + ], + "Description": "Compute fractional identity between trusted alignment and test alignment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "compalignp", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp", + "Galaxy wrapper version": "1.0", + "Conda id": "compalignp", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "coprarna", + "Galaxy tool ids": [ + "coprarna" + ], + "Description": "Target prediction for prokaryotic trans-acting small RNAs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/PatrickRWright/CopraRNA", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "coprarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/PatrickRWright/CopraRNA", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna", + "Galaxy wrapper version": "2.1.1", + "Conda id": "coprarna", + "Conda version": "2.1.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "dewseq", + "Galaxy tool ids": [ + "dewseq" + ], + "Description": "DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "CLIP-seq" + ], + "ToolShed id": "dewseq", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq", + "Galaxy wrapper version": "0.1.0+galaxy0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "dorina", + "Galaxy tool ids": [ + "dorina_search" + ], + "Description": "data source for RNA interactions in post-transcriptional regulation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA", + "Data Source" + ], + "ToolShed id": "dorina", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina", + "Galaxy wrapper version": "1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "dot2ct", + "Galaxy tool ids": [ + "rnastructure_dot2ct" + ], + "Description": "Dot-Bracket to Connect Table (CT)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "dot2ct", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct", + "Galaxy wrapper version": "5.7.a", + "Conda id": "rnastructure", + "Conda version": "6.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "dotknot", + "Galaxy tool ids": [ + "dotknot" + ], + "Description": "DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://dotknot.csse.uwa.edu.au/", + "ToolShed categories": [ + "RNA", + "Proteomics" + ], + "ToolShed id": "dotknot", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot", + "Galaxy wrapper version": "1.3.1", + "Conda id": "vienna_rna", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "exparna", + "Galaxy tool ids": [ + "exparna" + ], + "Description": "ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "exparna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna", + "Galaxy wrapper version": "1.0.1", + "Conda id": "exparna", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "graphprot", + "Galaxy tool ids": [ + "graphprot_predict_profile" + ], + "Description": "GraphProt models binding preferences of RNA-binding proteins.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/dmaticzka/GraphProt", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "CLIP-seq" + ], + "ToolShed id": "graphprot", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot", + "Galaxy wrapper version": "1.1.7+galaxy1", + "Conda id": "graphprot", + "Conda version": "1.1.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "htseq-clip", + "Galaxy tool ids": [ + "htseq_clip" + ], + "Description": "htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/EMBL-Hentze-group/htseq-clip", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "CLIP-seq" + ], + "ToolShed id": "htseq_clip", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip", + "Galaxy wrapper version": "0.1.0+galaxy0", + "Conda id": "htseq-clip", + "Conda version": "2.19.0b0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "infernal", + "Galaxy tool ids": [ + "infernal_cmalign", + "infernal_cmbuild", + "infernal_cmpress", + "infernal_cmscan", + "infernal_cmsearch", + "infernal_cmstat" + ], + "Description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities.", + "bio.tool id": "infernal", + "bio.tool ids": [ + "infernal" + ], + "biii": null, + "bio.tool name": "Infernal", + "bio.tool description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.", + "EDAM operation": [ + "Nucleic acid feature detection" + ], + "EDAM topic": [ + "Sequence sites, features and motifs", + "Structural genomics" + ], + "Status": "To update", + "Source": "http://infernal.janelia.org/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "infernal", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/infernal", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal", + "Galaxy wrapper version": "1.1.4", + "Conda id": "infernal", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [ + "Nucleic acid feature detection" + ], + "EDAM topic (no superclasses)": [ + "Sequence sites, features and motifs", + "Structural genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 6, + "Tools available on UseGalaxy.eu": 6, + "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": 6, + "Tools available on UseGalaxy.no": 6 + }, + { + "Galaxy wrapper id": "inforna", + "Galaxy tool ids": [], + "Description": "INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "inforna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "intarna", + "Galaxy tool ids": [ + "intarna" + ], + "Description": "Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/BackofenLab/IntaRNA", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "intarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna", + "Galaxy wrapper version": "3.4.0", + "Conda id": "intarna", + "Conda version": "3.4.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "kinwalker", + "Galaxy tool ids": [], + "Description": "Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.bioinf.uni-leipzig.de/Software/Kinwalker/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "kinwalker", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "locarna", + "Galaxy tool ids": [ + "locarna_exparnap", + "locarna_multiple", + "locarna_pairwise", + "locarna_pairwise_p", + "locarna_reliability_profile" + ], + "Description": "LocARNA - A suite for multiple alignment and folding of RNAs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.bioinf.uni-freiburg.de/Software/LocARNA/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "locarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna", + "Galaxy wrapper version": "1.9.2.3", + "Conda id": "locarna", + "Conda version": "2.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "mea", + "Galaxy tool ids": [ + "mea" + ], + "Description": "Maximum expected accuracy prediction", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.bioinf.uni-leipzig.de/Software/mea", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "mea", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea", + "Galaxy wrapper version": "0.6.4.1", + "Conda id": "mea", + "Conda version": "0.6.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "mqc", + "Galaxy tool ids": [ + "mqc" + ], + "Description": "Ribosome profiling mapping quality control tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Biobix/mQC", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mqc", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc", + "Galaxy wrapper version": "1.9", + "Conda id": "mqc", + "Conda version": "1.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "nastiseq", + "Galaxy tool ids": [ + "nastiseq" + ], + "Description": "A method to identify cis-NATs using ssRNA-seq", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "nastiseq", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq", + "Galaxy wrapper version": "1.0", + "Conda id": "r-nastiseq", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "paralyzer", + "Galaxy tool ids": [ + "paralyzer" + ], + "Description": "A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "paralyzer", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer", + "Galaxy wrapper version": "1.5", + "Conda id": "paralyzer", + "Conda version": "1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "pipmir", + "Galaxy tool ids": [ + "pipmir" + ], + "Description": "A method to identify novel plant miRNA.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "pipmir", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir", + "Galaxy wrapper version": "0.1.0", + "Conda id": "pipmir", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rRNA", + "Galaxy tool ids": [ + "meta_rna" + ], + "Description": "Identification of ribosomal RNA genes in metagenomic fragments.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://weizhong-lab.ucsd.edu/meta_rna/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rrna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rRNA", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA", + "Galaxy wrapper version": "0.1", + "Conda id": "hmmsearch3.0", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "rbpbench", + "Galaxy tool ids": [ + "rbpbench" + ], + "Description": "Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs", + "bio.tool id": "rbpbench", + "bio.tool ids": [ + "rbpbench" + ], + "biii": null, + "bio.tool name": "RBPBench", + "bio.tool description": "Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs", + "EDAM operation": [], + "EDAM topic": [ + "RNA", + "Protein interactions", + "RNA immunoprecipitation", + "Bioinformatics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/michauhl/RBPBench", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "CLIP-seq" + ], + "ToolShed id": "rbpbench", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench", + "Galaxy wrapper version": "0.8.1", + "Conda id": "rbpbench", + "Conda version": "0.8.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "RNA", + "Protein interactions", + "RNA immunoprecipitation", + "Bioinformatics", + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "rcas", + "Galaxy tool ids": [ + "rcas" + ], + "Description": "RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/BIMSBbioinfo/RCAS", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rcas", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas", + "Galaxy wrapper version": "1.5.4", + "Conda id": "bioconductor-rcas", + "Conda version": "1.28.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "reago", + "Galaxy tool ids": [ + "reago" + ], + "Description": "Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.", + "bio.tool id": "reago", + "bio.tool ids": [ + "reago" + ], + "biii": null, + "bio.tool name": "REAGO", + "bio.tool description": "This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.", + "EDAM operation": [ + "Sequence assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "RNA", + "Metagenomics", + "Microbiology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/chengyuan/reago-1.1", + "ToolShed categories": [ + "Metagenomics", + "RNA" + ], + "ToolShed id": "reago", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago", + "Galaxy wrapper version": "1.1", + "Conda id": "reago", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [ + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "RNA", + "Metagenomics", + "Microbiology" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "remurna", + "Galaxy tool ids": [ + "remurna" + ], + "Description": "remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "remurna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna", + "Galaxy wrapper version": "1.0.0", + "Conda id": "remurna", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "ribotaper", + "Galaxy tool ids": [ + "ribotaper_create_annotation", + "ribotaper_create_metaplots", + "ribotaper_ribosome_profiling" + ], + "Description": "A method for defining traslated ORFs using Ribosome Profiling data.", + "bio.tool id": "ribotaper", + "bio.tool ids": [ + "ribotaper" + ], + "biii": null, + "bio.tool name": "RiboTaper", + "bio.tool description": "New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.", + "EDAM operation": [ + "Gene expression profiling" + ], + "EDAM topic": [ + "Functional genomics" + ], + "Status": "To update", + "Source": "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "ribotaper", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper", + "Galaxy wrapper version": "1.3.1a", + "Conda id": "ribotaper", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [ + "Gene expression profiling" + ], + "EDAM topic (no superclasses)": [ + "Functional genomics" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 3, + "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": 3, + "Tools available on UseGalaxy.no": 3 + }, + { + "Galaxy wrapper id": "rna_shapes", + "Galaxy tool ids": [ + "RNAshapes" + ], + "Description": "Compute secondary structures of RNA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnashapes", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes", + "Galaxy wrapper version": "3.3.0", + "Conda id": "@EXECUTABLE@", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnabob", + "Galaxy tool ids": [ + "rbc_rnabob" + ], + "Description": "Fast pattern searching for RNA structural motifs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://eddylab.org/software.html", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnabob", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob", + "Galaxy wrapper version": "2.2.1.0", + "Conda id": "rnabob", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnacode", + "Galaxy tool ids": [ + "rbc_rnacode" + ], + "Description": "Analyze the protein coding potential in MSA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnacode", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode", + "Galaxy wrapper version": "0.3.2", + "Conda id": "rnacode", + "Conda version": "0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnacommender", + "Galaxy tool ids": [ + "rbc_rnacommender" + ], + "Description": "RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/gianlucacorrado/RNAcommender", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnacommender", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender", + "Galaxy wrapper version": "0.1.1", + "Conda id": "sam", + "Conda version": "3.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnalien", + "Galaxy tool ids": [ + "RNAlien" + ], + "Description": "RNAlien unsupervized RNA family model construction", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rna.tbi.univie.ac.at/rnalien/", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "rnalien", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien", + "Galaxy wrapper version": "1.3.6", + "Conda id": "rnalien", + "Conda version": "1.8.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnasnp", + "Galaxy tool ids": [ + "rnasnp" + ], + "Description": "RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rth.dk/resources/rnasnp/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnasnp", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp", + "Galaxy wrapper version": "1.2.0", + "Conda id": "rnasnp", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "rnaz", + "Galaxy tool ids": [ + "rnaz", + "rnaz_annotate", + "rnaz_cluster", + "rnaz_randomize_aln", + "rnaz_select_seqs", + "rnaz_window" + ], + "Description": "RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://www.tbi.univie.ac.at/~wash/RNAz/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "rnaz", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz", + "Galaxy wrapper version": "2.1.1", + "Conda id": "rnaz", + "Conda version": "2.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 6, + "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": 6, + "Tools available on UseGalaxy.no": 6 + }, + { + "Galaxy wrapper id": "selectsequencesfrommsa", + "Galaxy tool ids": [ + "selectsequencesfrommsa" + ], + "Description": "SelectSequences - selects representative entries from a multiple sequence alignment in clustal format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/eggzilla/SelectSequences", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "selectsequencesfrommsa", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa", + "Galaxy wrapper version": "1.0.5", + "Conda id": "selectsequencesfrommsa", + "Conda version": "1.0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "sortmerna", + "Galaxy tool ids": [ + "bg_sortmerna" + ], + "Description": "SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.", + "bio.tool id": "sortmerna", + "bio.tool ids": [ + "sortmerna" + ], + "biii": null, + "bio.tool name": "SortMeRNA", + "bio.tool description": "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.", + "EDAM operation": [ + "Sequence similarity search", + "Sequence comparison", + "Sequence alignment analysis" + ], + "EDAM topic": [ + "Metatranscriptomics", + "Metagenomics" + ], + "Status": "To update", + "Source": "http://bioinfo.lifl.fr/RNA/sortmerna/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "sortmerna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna", + "Galaxy wrapper version": "4.3.6", + "Conda id": "sortmerna", + "Conda version": "4.3.7", + "EDAM operation (no superclasses)": [ + "Sequence similarity search", + "Sequence alignment analysis" + ], + "EDAM topic (no superclasses)": [ + "Metatranscriptomics", + "Metagenomics" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "sshmm", + "Galaxy tool ids": [ + "sshmm" + ], + "Description": "ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.molgen.mpg.de/heller/ssHMM", + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "sshmm", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm", + "Galaxy wrapper version": "1.0.7", + "Conda id": "sshmm", + "Conda version": "1.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "targetfinder", + "Galaxy tool ids": [ + "targetfinder" + ], + "Description": "Plant small RNA target prediction tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/carringtonlab/TargetFinder.git", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "targetfinder", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder", + "Galaxy wrapper version": "1.7", + "Conda id": "targetfinder", + "Conda version": "1.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "trna_prediction", + "Galaxy tool ids": [ + "aragorn_trna", + "trnascan" + ], + "Description": "Aragorn predicts tRNA and tmRNA in nucleotide sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://mbioserv2.mbioekol.lu.se/ARAGORN/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "trna_prediction", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction", + "Galaxy wrapper version": "0.6", + "Conda id": "aragorn", + "Conda version": "1.2.41", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 2, + "Tools available on UseGalaxy.eu": 2, + "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)": 2, + "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": 2, + "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": 2, + "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": 2 + }, + { + "Galaxy wrapper id": "vienna_rna", + "Galaxy tool ids": [ + "viennarna_kinfold", + "viennarna_kinwalker", + "viennarna_rna2dfold", + "viennarna_rnaaliduplex", + "viennarna_rnaalifold", + "viennarna_rnacofold", + "viennarna_rnadistance", + "viennarna_rnaduplex", + "viennarna_rnaeval", + "viennarna_rnafold", + "viennarna_rnaheat", + "viennarna_rnainverse", + "viennarna_rnalalifold", + "viennarna_rnalfold", + "viennarna_rnapaln", + "viennarna_rnadpdist", + "viennarna_rnapkplex", + "viennarna_rnaplex", + "viennarna_rnaplfold", + "viennarna_rnaplot", + "viennarna_rnasnoop", + "viennarna_rnasubopt", + "viennarna_rnaup" + ], + "Description": "ViennaRNA - Prediction and comparison of RNA secondary structures", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.tbi.univie.ac.at/RNA/", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "viennarna", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna", + "Galaxy wrapper version": "2.2.10", + "Conda id": "viennarna", + "Conda version": "2.6.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 21, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 21, + "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": 21, + "Tools available on UseGalaxy.no": 21 + }, + { + "Galaxy wrapper id": "sailfish", + "Galaxy tool ids": [ + "sailfish" + ], + "Description": "Sailfish is a tool for transcript quantification from RNA-seq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.cs.cmu.edu/~ckingsf/software/sailfish/", + "ToolShed categories": [ + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "sailfish", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sailfish", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sailfish", + "Galaxy wrapper version": "0.10.1.1", + "Conda id": "bzip2", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "salmon", + "Galaxy tool ids": [ + "alevin", + "salmon", + "salmonquantmerge" + ], + "Description": "Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.", + "bio.tool id": "salmon", + "bio.tool ids": [ + "salmon" + ], + "biii": null, + "bio.tool name": "Salmon", + "bio.tool description": "A tool for transcript expression quantification from RNA-seq data", + "EDAM operation": [ + "Sequence composition calculation", + "RNA-Seq quantification", + "Gene expression analysis" + ], + "EDAM topic": [ + "RNA-Seq", + "Gene expression", + "Transcriptomics" + ], + "Status": "To update", + "Source": "https://github.com/COMBINE-lab/salmon", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/salmon", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/salmon", + "Galaxy wrapper version": "1.10.1", + "Conda id": "salmon", + "Conda version": "1.10.3", + "EDAM operation (no superclasses)": [ + "Sequence composition calculation", + "RNA-Seq quantification", + "Gene expression analysis" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Transcriptomics" + ], + "Available on UseGalaxy.org (Main)": 2, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 2, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 3, + "Tools available on UseGalaxy.fr": 1, + "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": 2, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 3, + "Tools available on UseGalaxy.cz": 3, + "Tools available on UseGalaxy.no": 3 + }, + { + "Galaxy wrapper id": "sambamba", + "Galaxy tool ids": [ + "sambamba_flagstat", + "sambamba_markdup", + "sambamba_merge", + "sambamba_slice", + "sambamba_sort", + "sambamba_view", + "sambamba_depth" + ], + "Description": "SAMBAMBA: process your BAM data faster!", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/lomereiter/sambamba", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "sambamba", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sambamba", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sambamba", + "Galaxy wrapper version": null, + "Conda id": "sambamba", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "sed", + "Galaxy tool ids": [ + "sed_stream_editor" + ], + "Description": "Manipulate your data with the sed command line tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "sed_wrapper", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sed", + "Galaxy wrapper version": "0.0.1", + "Conda id": "sed", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "segemehl", + "Galaxy tool ids": [ + "segemehl" + ], + "Description": "segemehl - short read mapping with gaps", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.bioinf.uni-leipzig.de/Software/segemehl/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "segemehl", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/segemehl", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/segemehl", + "Galaxy wrapper version": "0.2.0.4", + "Conda id": "segemehl", + "Conda version": "0.3.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "sklearn", + "Galaxy tool ids": [ + "sklearn_mlxtend_association_rules", + "sklearn_clf_metrics", + "sklearn_discriminant_classifier", + "sklearn_ensemble", + "sklearn_estimator_attributes", + "sklearn_feature_selection", + "sklearn_fitted_model_eval", + "sklearn_generalized_linear", + "keras_batch_models", + "keras_model_builder", + "keras_model_config", + "keras_train_and_eval", + "sklearn_label_encoder", + "sklearn_lightgbm", + "ml_visualization_ex", + "model_prediction", + "sklearn_model_validation", + "sklearn_nn_classifier", + "sklearn_numeric_clustering", + "sklearn_pairwise_metrics", + "sklearn_pca", + "sklearn_build_pipeline", + "sklearn_data_preprocess", + "sklearn_regression_metrics", + "sklearn_sample_generator", + "sklearn_searchcv", + "sklearn_model_fit", + "scipy_sparse", + "stacking_ensemble_models", + "sklearn_svm_classifier", + "sklearn_to_categorical", + "sklearn_train_test_eval", + "sklearn_train_test_split" + ], + "Description": "Machine Learning tool suite from Scikit-learn", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://scikit-learn.org", + "ToolShed categories": [ + "Machine Learning", + "Statistics" + ], + "ToolShed id": "sklearn", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/sklearn", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/sklearn", + "Galaxy wrapper version": "1.0.11.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 30, + "Available on UseGalaxy.org.au": 14, + "Available on UseGalaxy.eu": 31, + "Available on UseGalaxy.fr": 16, + "Tools available on UseGalaxy.org (Main)": 30, + "Tools available on UseGalaxy.org.au": 14, + "Tools available on UseGalaxy.eu": 31, + "Tools available on UseGalaxy.fr": 16, + "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": 29, + "Tools available on UseGalaxy.cz": 31, + "Tools available on UseGalaxy.no": 27 + }, + { + "Galaxy wrapper id": "splitfasta", + "Galaxy tool ids": [ + "rbc_splitfasta" + ], + "Description": "Split a multi-sequence fasta file into files containing single sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "splitfasta", + "Galaxy wrapper owner": "rnateam", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta", + "Galaxy wrapper version": "0.4.0", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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)": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "statistics", + "Galaxy tool ids": [ + "bg_statistical_hypothesis_testing" + ], + "Description": "Tool for computing statistical tests.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "bg_statistical_hypothesis_testing", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/statistics", + "Galaxy wrapper version": "0.3", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "stress_ng", + "Galaxy tool ids": [ + "stress_ng" + ], + "Description": "stress test a computer system in various selectable ways", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Web Services" + ], + "ToolShed id": "stress_ng", + "Galaxy wrapper owner": "bgruening-util", + "Galaxy wrapper source": "https://github.com/ColinIanKing/stress-ng", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng", + "Galaxy wrapper version": "0.12.04", + "Conda id": "stress-ng", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "tapscan", + "Galaxy tool ids": [ + "tapscan_classify" + ], + "Description": "Search for transcription associated proteins (TAPs)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://plantcode.cup.uni-freiburg.de/tapscan/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "tapscan", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tapscan", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tapscan", + "Galaxy wrapper version": "4.76+galaxy0", + "Conda id": "hmmer", + "Conda version": "3.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "add_line_to_file", + "Galaxy tool ids": [ + "add_line_to_file" + ], + "Description": "Adds a text line to the beginning or end of a file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "add_line_to_file", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file", + "Galaxy wrapper version": "0.1.0", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "column_arrange_by_header", + "Galaxy tool ids": [ + "bg_column_arrange_by_header" + ], + "Description": "Column arrange by header name", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "column_arrange_by_header", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header", + "Galaxy wrapper version": "0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "join_files_on_column_fuzzy", + "Galaxy tool ids": [ + "join_files_on_column_fuzzy" + ], + "Description": "Join two files on a common column, allowing a certain difference.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "join_files_on_column_fuzzy", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "split_file_on_column", + "Galaxy tool ids": [ + "tp_split_on_column" + ], + "Description": "Split a file on a specific column.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "split_file_on_column", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column", + "Galaxy wrapper version": "0.6", + "Conda id": "gawk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "split_file_to_collection", + "Galaxy tool ids": [ + "split_file_to_collection" + ], + "Description": "Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "split_file_to_collection", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection", + "Galaxy wrapper version": "0.5.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "text_processing", + "Galaxy tool ids": [ + "tp_awk_tool", + "tp_cat", + "tp_cut_tool", + "tp_easyjoin_tool", + "tp_find_and_replace", + "tp_grep_tool", + "tp_head_tool", + "tp_multijoin_tool", + "nl", + "tp_text_file_with_recurring_lines", + "tp_replace_in_column", + "tp_replace_in_line", + "tp_sed_tool", + "tp_sort_header_tool", + "tp_sort_rows", + "tp_uniq_tool", + "tp_tac", + "tp_tail_tool", + "tp_unfold_column_tool", + "tp_sorted_uniq" + ], + "Description": "High performance text processing tools using the GNU coreutils, sed, awk and friends.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.gnu.org/software/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "text_processing", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing", + "Galaxy wrapper version": "9.3", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 20, + "Available on UseGalaxy.org.au": 20, + "Available on UseGalaxy.eu": 20, + "Available on UseGalaxy.fr": 20, + "Tools available on UseGalaxy.org (Main)": 20, + "Tools available on UseGalaxy.org.au": 20, + "Tools available on UseGalaxy.eu": 20, + "Tools available on UseGalaxy.fr": 20, + "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": 19, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 19, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 19, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 20, + "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": 19, + "Tools available on UseGalaxy.cz": 19, + "Tools available on UseGalaxy.no": 19 + }, + { + "Galaxy wrapper id": "tgsgapcloser", + "Galaxy tool ids": [ + "tgsgapcloser" + ], + "Description": "TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.", + "bio.tool id": "TGS-GapCloser", + "bio.tool ids": [ + "TGS-GapCloser" + ], + "biii": null, + "bio.tool name": "TGS-GapCloser", + "bio.tool description": "TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.", + "EDAM operation": [ + "Genome assembly", + "Read mapping", + "Scaffolding", + "Localised reassembly" + ], + "EDAM topic": [ + "Sequencing", + "Sequence assembly", + "Phylogeny", + "Transcription factors and regulatory sites", + "Mapping" + ], + "Status": "To update", + "Source": "https://github.com/BGI-Qingdao/TGS-GapCloser", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "tgsgapcloser", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser", + "Galaxy wrapper version": "1.0.3", + "Conda id": "tgsgapcloser", + "Conda version": "1.2.1", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Read mapping", + "Scaffolding", + "Localised reassembly" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence assembly", + "Phylogeny", + "Transcription factors and regulatory sites", + "Mapping" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "tiara", + "Galaxy tool ids": [ + "tiara" + ], + "Description": "Tool for identification of eukaryotic sequences in the metagenomic datasets.", + "bio.tool id": "Tiara", + "bio.tool ids": [ + "Tiara" + ], + "biii": null, + "bio.tool name": "TIARA", + "bio.tool description": "Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).", + "EDAM operation": [ + "Genome comparison", + "Data retrieval", + "Variant calling", + "Genome visualisation", + "Structural variation detection" + ], + "EDAM topic": [ + "Sequencing", + "Genomics", + "DNA polymorphism", + "DNA structural variation" + ], + "Status": "To update", + "Source": "https://github.com/ibe-uw/tiara", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": "tiara", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/tiara", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tiara", + "Galaxy wrapper version": "1.0.3", + "Conda id": "tiara", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Genome comparison", + "Data retrieval", + "Variant calling", + "Genome visualisation", + "Structural variation detection" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Genomics", + "DNA polymorphism" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "tool_recommendation_model", + "Galaxy tool ids": [ + "create_tool_recommendation_model" + ], + "Description": "Create model to recommend tools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "create_tool_recommendation_model", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model", + "Galaxy wrapper version": "0.0.5", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "trim_galore", + "Galaxy tool ids": [ + "trim_galore" + ], + "Description": "Trim Galore adaptive quality and adapter trimmer", + "bio.tool id": "trim_galore", + "bio.tool ids": [ + "trim_galore" + ], + "biii": null, + "bio.tool name": "Trim Galore", + "bio.tool description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.", + "EDAM operation": [ + "Sequence trimming", + "Primer removal", + "Read pre-processing" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", + "ToolShed categories": [ + "Sequence Analysis", + "Fastq Manipulation" + ], + "ToolShed id": "trim_galore", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore", + "Galaxy wrapper version": "0.6.7", + "Conda id": "trim-galore", + "Conda version": "0.6.10", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "Primer removal", + "Read pre-processing" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 0, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "uniprot_rest_interface", + "Galaxy tool ids": [ + "uniprot" + ], + "Description": "UniProt ID mapping and sequence retrieval", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/jdrudolph/uniprot", + "ToolShed categories": [ + "Proteomics", + "Sequence Analysis" + ], + "ToolShed id": "uniprot_rest_interface", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface", + "Galaxy wrapper version": "0.5", + "Conda id": "requests", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "vt", + "Galaxy tool ids": [ + "vt_@BINARY@", + "vt_@BINARY@" + ], + "Description": "A tool set for short variant discovery in genetic sequence data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "vt", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/atks/vt", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/vt", + "Galaxy wrapper version": "0.2", + "Conda id": "vt", + "Conda version": "2015.11.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "whisper", + "Galaxy tool ids": [ + "whisper" + ], + "Description": "Transcribe audio or video files to text using the OpenAI Whisper.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "whisper", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/whisper", + "Galaxy wrapper version": "20231117", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": "wtdbg", + "Galaxy tool ids": [ + "wtdbg" + ], + "Description": "WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.", + "bio.tool id": "wtdbg2", + "bio.tool ids": [ + "wtdbg2" + ], + "biii": null, + "bio.tool name": "wtdbg2", + "bio.tool description": "Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.", + "EDAM operation": [ + "Genome assembly", + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ruanjue/wtdbg2", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "wtdbg", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg", + "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg", + "Galaxy wrapper version": "2.5", + "Conda id": "wtdbg", + "Conda version": "2.5", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Sequencing" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "align_back_trans", + "Galaxy tool ids": [ + "align_back_trans" + ], + "Description": "Thread nucleotides onto a protein alignment (back-translation)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "align_back_trans", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans", + "Galaxy wrapper version": "0.0.10", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "chromosome_diagram", + "Galaxy tool ids": [ + "chromosome_diagram" + ], + "Description": "Chromosome Diagrams using Biopython", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics", + "Sequence Analysis", + "Visualization" + ], + "ToolShed id": "chromosome_diagram", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram", + "Galaxy wrapper version": "0.0.3", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "clc_assembly_cell", + "Galaxy tool ids": [ + "clc_assembler", + "clc_mapper" + ], + "Description": "Galaxy wrapper for the CLC Assembly Cell suite from CLCBio", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", + "ToolShed categories": [ + "Assembly", + "Next Gen Mappers", + "SAM" + ], + "ToolShed id": "clc_assembly_cell", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell", + "Galaxy wrapper version": "0.0.7", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "clinod", + "Galaxy tool ids": [ + "clinod" + ], + "Description": "NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins", + "bio.tool id": "clinod", + "bio.tool ids": [ + "clinod" + ], + "biii": null, + "bio.tool name": "clinod", + "bio.tool description": "The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.", + "EDAM operation": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.compbio.dundee.ac.uk/www-nod/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "clinod", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod", + "Galaxy wrapper version": "0.1.0", + "Conda id": "clinod", + "Conda version": "1.3", + "EDAM operation (no superclasses)": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "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": "count_roi_variants", + "Galaxy tool ids": [ + "count_roi_variants" + ], + "Description": "Count sequence variants in region of interest in BAM file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", + "ToolShed categories": [ + "Assembly", + "SAM" + ], + "ToolShed id": "count_roi_variants", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants", + "Galaxy wrapper version": "0.0.6", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "coverage_stats", + "Galaxy tool ids": [ + "coverage_stats" + ], + "Description": "BAM coverage statistics using samtools idxstats and depth", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", + "ToolShed categories": [ + "Assembly", + "SAM" + ], + "ToolShed id": "coverage_stats", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats", + "Galaxy wrapper version": "0.1.0", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "effectiveT3", + "Galaxy tool ids": [ + "effectiveT3" + ], + "Description": "Find bacterial type III effectors in protein sequences", + "bio.tool id": "effectivet3", + "bio.tool ids": [ + "effectivet3" + ], + "biii": null, + "bio.tool name": "EffectiveT3", + "bio.tool description": "Prediction of putative Type-III secreted proteins.", + "EDAM operation": [ + "Sequence classification" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://effectors.org", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "effectivet3", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3", + "Galaxy wrapper version": "0.0.21", + "Conda id": "effectiveT3", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [ + "Sequence classification" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "fasta_filter_by_id", + "Galaxy tool ids": [ + "fasta_filter_by_id" + ], + "Description": "Filter FASTA sequences by ID (DEPRECATED)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "fasta_filter_by_id", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id", + "Galaxy wrapper version": "0.0.7", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "fastq_filter_by_id", + "Galaxy tool ids": [ + "fastq_filter_by_id" + ], + "Description": "Filter FASTQ sequences by ID (DEPRECATED)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "fastq_filter_by_id", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id", + "Galaxy wrapper version": "0.0.7", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "fastq_pair_names", + "Galaxy tool ids": [ + "fastq_pair_names" + ], + "Description": "Extract FASTQ paired read names", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fastq_pair_names", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names", + "Galaxy wrapper version": "0.0.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "fastq_paired_unpaired", + "Galaxy tool ids": [ + "fastq_paired_unpaired" + ], + "Description": "Divide FASTQ file into paired and unpaired reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", + "ToolShed categories": [ + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "fastq_paired_unpaired", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired", + "Galaxy wrapper version": "0.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "get_orfs_or_cdss", + "Galaxy tool ids": [ + "get_orfs_or_cdss" + ], + "Description": "Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "get_orfs_or_cdss", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss", + "Galaxy wrapper version": "0.2.3", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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)": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 0 + }, + { + "Galaxy wrapper id": "mummer", + "Galaxy tool ids": [ + "mummerplot_wrapper" + ], + "Description": "Draw dotplots using mummer, mucmer, or promer with mummerplot", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://mummer.sourceforge.net/", + "ToolShed categories": [ + "Graphics", + "Sequence Analysis", + "Visualization" + ], + "ToolShed id": "mummer", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer", + "Galaxy wrapper version": "0.0.8", + "Conda id": "ghostscript", + "Conda version": "9.18", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "nlstradamus", + "Galaxy tool ids": [ + "nlstradamus" + ], + "Description": "Find nuclear localization signals (NLSs) in protein sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.moseslab.csb.utoronto.ca/NLStradamus", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "nlstradamus", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus", + "Galaxy wrapper version": "0.0.11", + "Conda id": "NLStradamus", + "Conda version": "1.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "predictnls", + "Galaxy tool ids": [ + "predictnls" + ], + "Description": "Python reimplementation of predictNLS for Galaxy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "predictnls", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls", + "Galaxy wrapper version": "0.0.10", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "protein_analysis", + "Galaxy tool ids": [ + "promoter2", + "Psortb", + "rxlr_motifs", + "signalp3", + "tmhmm2", + "wolf_psort" + ], + "Description": "TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tmhmm_and_signalp", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis", + "Galaxy wrapper version": "0.0.13", + "Conda id": "promoter", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 6, + "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": 6, + "Tools available on UseGalaxy.cz": 6, + "Tools available on UseGalaxy.no": 6 + }, + { + "Galaxy wrapper id": "sample_seqs", + "Galaxy tool ids": [ + "sample_seqs" + ], + "Description": "Sub-sample sequences files (e.g. to reduce coverage)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", + "ToolShed categories": [ + "Assembly", + "Fasta Manipulation", + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "sample_seqs", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs", + "Galaxy wrapper version": "0.2.6", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "samtools_depad", + "Galaxy tool ids": [ + "samtools_depad" + ], + "Description": "Re-align a SAM/BAM file with a padded reference (using samtools depad)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.htslib.org/", + "ToolShed categories": [ + "Assembly", + "SAM", + "Sequence Analysis" + ], + "ToolShed id": "samtools_depad", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad", + "Galaxy wrapper version": "0.0.5", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "samtools_depth", + "Galaxy tool ids": [ + "samtools_depth" + ], + "Description": "Coverage depth via samtools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.htslib.org/", + "ToolShed categories": [ + "Assembly", + "Sequence Analysis", + "SAM" + ], + "ToolShed id": "samtools_depth", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth", + "Galaxy wrapper version": "0.0.3", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "samtools_idxstats", + "Galaxy tool ids": [ + "samtools_idxstats" + ], + "Description": "BAM mapping statistics (using samtools idxstats)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.htslib.org/", + "ToolShed categories": [ + "Assembly", + "Next Gen Mappers", + "SAM" + ], + "ToolShed id": "samtools_idxstats", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats", + "Galaxy wrapper version": "0.0.6", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "Tools available on ANASTASIA": 0, + "Tools available on APOSTL": 0, + "Tools available on ARGs-OAP": 0, + "Tools available on BF2I-MAP": 1, + "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": 1, + "Tools available on Galaxy@Pasteur": 1, + "Tools available on GalaxyTrakr": 1, + "Tools available on Genomic Hyperbrowser": 0, + "Tools available on GigaGalaxy": 0, + "Tools available on HyPhy HIV NGS Tools": 1, + "Tools available on IPK Galaxy Blast Suite": 0, + "Tools available on ImmPort Galaxy": 0, + "Tools available on InteractoMIX": 0, + "Tools available on MISSISSIPPI": 1, + "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": 1, + "Tools available on UseGalaxy.cz": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "seq_composition", + "Galaxy tool ids": [ + "seq_composition" + ], + "Description": "Sequence composition", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seq_composition", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition", + "Galaxy wrapper version": "0.0.5", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "seq_filter_by_id", + "Galaxy tool ids": [ + "seq_filter_by_id" + ], + "Description": "Filter sequences by ID", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "seq_filter_by_id", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id", + "Galaxy wrapper version": "0.2.9", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 1, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "seq_filter_by_mapping", + "Galaxy tool ids": [ + "seq_filter_by_mapping" + ], + "Description": "Filter sequencing reads using SAM/BAM mapping files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", + "ToolShed categories": [ + "Assembly", + "Fasta Manipulation", + "Fastq Manipulation", + "SAM", + "Sequence Analysis" + ], + "ToolShed id": "seq_filter_by_mapping", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping", + "Galaxy wrapper version": "0.0.8", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "seq_length", + "Galaxy tool ids": [ + "seq_length" + ], + "Description": "Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "seq_length", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length", + "Galaxy wrapper version": "0.0.5", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": "seq_primer_clip", + "Galaxy tool ids": [ + "seq_primer_clip" + ], + "Description": "Trim off 5' or 3' primers", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "ToolShed categories": [ + "Assembly", + "Fasta Manipulation", + "Text Manipulation" + ], + "ToolShed id": "seq_primer_clip", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip", + "Galaxy wrapper version": "0.0.18", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": "seq_rename", + "Galaxy tool ids": [ + "seq_rename" + ], + "Description": "Rename sequences with ID mapping from a tabular file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "seq_rename", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename", + "Galaxy wrapper version": "0.0.10", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 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": 1, + "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": 1 + }, + { + "Galaxy wrapper id": "seq_select_by_id", + "Galaxy tool ids": [ + "seq_select_by_id" + ], + "Description": "Select sequences by ID", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "seq_select_by_id", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id", + "Galaxy wrapper version": "0.0.15", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.fr": 0, + "Tools available on UseGalaxy.org (Main)": 0, + "Tools available on UseGalaxy.org.au": 1, + "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": 1, + "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": "venn_list", + "Galaxy tool ids": [ + "venn_list" + ], + "Description": "Draw Venn Diagram (PDF) from lists, FASTA files, etc", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "ToolShed categories": [ + "Graphics", + "Sequence Analysis", + "Visualization" + ], + "ToolShed id": "venn_list", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list", + "Galaxy wrapper version": "0.1.2", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org (Main)": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.fr": 1, + "Tools available on UseGalaxy.org (Main)": 1, + "Tools available on UseGalaxy.org.au": 0, + "Tools available on UseGalaxy.eu": 1, + "Tools available on UseGalaxy.fr": 1, + "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": 1, + "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": 1, + "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": 1, + "Tools available on UseGalaxy.no": 1 + }, + { + "Galaxy wrapper id": "TrimNs", + "Galaxy tool ids": [ + "trimns" + ], + "Description": "TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "trimns", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs", + "Galaxy wrapper version": "0.1.0", + "Conda id": "trimns_vgp", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "abricate", + "Galaxy tool ids": [ + "abricate", + "abricate_list", + "abricate_summary" + ], + "Description": "Mass screening of contigs for antiobiotic resistance genes", + "bio.tool id": "ABRicate", + "bio.tool ids": [ + "ABRicate" + ], + "biii": null, + "bio.tool name": "ABRicate", + "bio.tool description": "Mass screening of contigs for antimicrobial resistance or virulence genes.", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Genomics", + "Microbiology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/abricate", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "abricate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate", + "Galaxy wrapper version": "1.0.1", + "Conda id": "abricate", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Microbiology" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "abritamr", + "Galaxy tool ids": [ + "abritamr" + ], + "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", + "bio.tool id": "abritamr", + "bio.tool ids": [ + "abritamr" + ], + "biii": null, + "bio.tool name": "abriTAMR", + "bio.tool description": "an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Microbiology", + "Public health and epidemiology", + "Infectious disease" + ], + "Status": "To update", + "Source": "https://zenodo.org/record/7370628", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "abritamr", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", + "Galaxy wrapper version": "1.0.14", + "Conda id": "abritamr", + "Conda version": "1.0.17", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Public health and epidemiology", + "Infectious disease" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "abyss", + "Galaxy tool ids": [ + "abyss-pe" + ], + "Description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", + "bio.tool id": "abyss", + "bio.tool ids": [ + "abyss" + ], + "biii": null, + "bio.tool name": "ABySS", + "bio.tool description": "De novo genome sequence assembler using short reads.", + "EDAM operation": [ + "Genome assembly", + "De-novo assembly", + "Scaffolding" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "http://www.bcgsc.ca/platform/bioinfo/software/abyss", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "abyss", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", + "Galaxy wrapper version": "2.3.7", + "Conda id": "abyss", + "Conda version": "2.3.7", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "De-novo assembly", + "Scaffolding" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "adapter_removal", + "Galaxy tool ids": [ + "adapter_removal" + ], + "Description": "Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.", + "bio.tool id": "adapterremoval", + "bio.tool ids": [ + "adapterremoval" + ], + "biii": null, + "bio.tool name": "AdapterRemoval", + "bio.tool description": "AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.", + "EDAM operation": [ + "Sequence trimming", + "Sequence merging", + "Primer removal" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/MikkelSchubert/adapterremoval", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "adapter_removal", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal", + "Galaxy wrapper version": "2.3.3", + "Conda id": "adapterremoval", + "Conda version": "2.3.3", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "Sequence merging", + "Primer removal" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "add_input_name_as_column", + "Galaxy tool ids": [ + "addName" + ], + "Description": "Add input name as column on an existing tabular file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "add_input_name_as_column", + "Galaxy wrapper owner": "mvdbeek", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "aegean", + "Galaxy tool ids": [ + "aegean_canongff3", + "aegean_gaeval", + "aegean_locuspocus", + "aegean_parseval" + ], + "Description": "AEGeAn toolkit wrappers", + "bio.tool id": "gaeval", + "bio.tool ids": [ + "gaeval" + ], + "biii": null, + "bio.tool name": "GAEVAL", + "bio.tool description": "Gene Annotation EVAluation.", + "EDAM operation": [ + "Sequence annotation" + ], + "EDAM topic": [ + "Sequence analysis", + "Gene structure" + ], + "Status": "Up-to-date", + "Source": "https://github.com/BrendelGroup/AEGeAn", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "aegean", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean", + "Galaxy wrapper version": "0.16.0", + "Conda id": "aegean", + "Conda version": "0.16.0", + "EDAM operation (no superclasses)": [ + "Sequence annotation" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Gene structure" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "aldex2", + "Galaxy tool ids": [ + "aldex2" + ], + "Description": "Performs analysis Of differential abundance taking sample variation into account", + "bio.tool id": "aldex2", + "bio.tool ids": [ + "aldex2" + ], + "biii": null, + "bio.tool name": "ALDEx2", + "bio.tool description": "A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.", + "EDAM operation": [ + "Statistical inference" + ], + "EDAM topic": [ + "Gene expression", + "Statistics and probability" + ], + "Status": "To update", + "Source": "https://github.com/ggloor/ALDEx_bioc", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "aldex2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", + "Galaxy wrapper version": "1.26.0", + "Conda id": "bioconductor-aldex2", + "Conda version": "1.34.0", + "EDAM operation (no superclasses)": [ + "Statistical inference" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "allegro", + "Galaxy tool ids": [ + "allegro" + ], + "Description": "Linkage and haplotype analysis from deCODE", + "bio.tool id": "allegro", + "bio.tool ids": [ + "allegro" + ], + "biii": null, + "bio.tool name": "Allegro", + "bio.tool description": "It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.", + "EDAM operation": [ + "Sequence motif discovery" + ], + "EDAM topic": [ + "Sequence analysis", + "Transcription factors and regulatory sites", + "DNA" + ], + "Status": "To update", + "Source": "http://www.decode.com/software/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "allegro", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro", + "Galaxy wrapper version": "@VER@.0", + "Conda id": "allegro", + "Conda version": "3", + "EDAM operation (no superclasses)": [ + "Sequence motif discovery" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Transcription factors and regulatory sites", + "DNA" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "amplican", + "Galaxy tool ids": [ + "amplican" + ], + "Description": "AmpliCan is an analysis tool for genome editing.", + "bio.tool id": "amplican", + "bio.tool ids": [ + "amplican" + ], + "biii": null, + "bio.tool name": "amplican", + "bio.tool description": "It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.", + "EDAM operation": [ + "Alignment", + "Standardisation and normalisation" + ], + "EDAM topic": [ + "PCR experiment", + "Statistics and probability" + ], + "Status": "To update", + "Source": "https://github.com/valenlab/amplican", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "amplican", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican", + "Galaxy wrapper version": "1.14.0", + "Conda id": "bioconductor-amplican", + "Conda version": "1.24.0", + "EDAM operation (no superclasses)": [ + "Alignment", + "Standardisation and normalisation" + ], + "EDAM topic (no superclasses)": [ + "PCR experiment", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ampvis2", + "Galaxy tool ids": [ + "ampvis2_alpha_diversity", + "ampvis2_boxplot", + "ampvis2_core", + "ampvis2_export_fasta", + "ampvis2_frequency", + "ampvis2_heatmap", + "ampvis2_load", + "ampvis2_merge_ampvis2", + "ampvis2_mergereplicates", + "ampvis2_octave", + "ampvis2_ordinate", + "ampvis2_otu_network", + "ampvis2_rankabundance", + "ampvis2_rarecurve", + "ampvis2_setmetadata", + "ampvis2_subset_samples", + "ampvis2_subset_taxa", + "ampvis2_timeseries", + "ampvis2_venn" + ], + "Description": "ampvis2", + "bio.tool id": "ampvis", + "bio.tool ids": [ + "ampvis" + ], + "biii": null, + "bio.tool name": "ampvis", + "bio.tool description": "ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.", + "EDAM operation": [ + "Analysis", + "Visualisation" + ], + "EDAM topic": [ + "Biodiversity" + ], + "Status": "To update", + "Source": "https://github.com/MadsAlbertsen/ampvis2/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "ampvis2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2", + "Galaxy wrapper version": "2.8.6", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Analysis", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Biodiversity" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 19, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "amrfinderplus", + "Galaxy tool ids": [ + "amrfinderplus" + ], + "Description": "\"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search \"plus\", stress, heat, and biocide resistance and virulence factors for some organisms.", + "bio.tool id": "amrfinderplus", + "bio.tool ids": [ + "amrfinderplus" + ], + "biii": null, + "bio.tool name": "AMRFinderPlus", + "bio.tool description": "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search \"plus\", stress, heat, and biocide resistance and virulence factors for some organisms", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Microbiology", + "Public health and epidemiology", + "Infectious disease" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ncbi/amr", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "AMRFinderPlus", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus", + "Galaxy wrapper version": "3.12.8", + "Conda id": "ncbi-amrfinderplus", + "Conda version": "3.12.8", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Public health and epidemiology", + "Infectious disease" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ancombc", + "Galaxy tool ids": [ + "ancombc" + ], + "Description": "Performs analysis of compositions of microbiomes with bias correction.", + "bio.tool id": "ancombc", + "bio.tool ids": [ + "ancombc" + ], + "biii": null, + "bio.tool name": "ANCOMBC", + "bio.tool description": "Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.", + "EDAM operation": [ + "DNA barcoding" + ], + "EDAM topic": [ + "Microbial ecology", + "Metagenomics", + "Taxonomy" + ], + "Status": "To update", + "Source": "https://github.com/FrederickHuangLin/ANCOMBC", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "ancombc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc", + "Galaxy wrapper version": "1.4.0", + "Conda id": "bioconductor-ancombc", + "Conda version": "2.4.0", + "EDAM operation (no superclasses)": [ + "DNA barcoding" + ], + "EDAM topic (no superclasses)": [ + "Microbial ecology", + "Metagenomics", + "Taxonomy" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "anndata", + "Galaxy tool ids": [ + "anndata_export", + "anndata_import", + "anndata_inspect", + "anndata_manipulate", + "modify_loom" + ], + "Description": "Import, Export, Inspect and Manipulate Anndata and Loom objects", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://anndata.readthedocs.io", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "anndata", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata", + "Galaxy wrapper version": "0.10.3", + "Conda id": "anndata", + "Conda version": "0.6.22.post1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "annotatemyids", + "Galaxy tool ids": [ + "annotatemyids" + ], + "Description": "annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages", + "bio.tool id": "annotatemyids", + "bio.tool ids": [ + "annotatemyids" + ], + "biii": null, + "bio.tool name": "annotatemyids", + "bio.tool description": "This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.", + "EDAM operation": [ + "Annotation" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "annotatemyids", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids", + "Galaxy wrapper version": "3.18.0", + "Conda id": "bioconductor-org.hs.eg.db", + "Conda version": "3.18.0", + "EDAM operation (no superclasses)": [ + "Annotation" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "arriba", + "Galaxy tool ids": [ + "arriba", + "arriba_draw_fusions", + "arriba_get_filters" + ], + "Description": "Arriba detects fusion genes in RNA-Seq data after running RNA-STAR", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/suhrig/arriba", + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics" + ], + "ToolShed id": "arriba", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba", + "Galaxy wrapper version": "2.4.0", + "Conda id": "arriba", + "Conda version": "2.4.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "art", + "Galaxy tool ids": [ + "art_454", + "art_illumina", + "art_solid" + ], + "Description": "Simulator for Illumina, 454, and SOLiD sequencing data", + "bio.tool id": "art", + "bio.tool ids": [ + "art" + ], + "biii": null, + "bio.tool name": "ART", + "bio.tool description": "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD", + "EDAM operation": [ + "Conversion" + ], + "EDAM topic": [ + "Bioinformatics" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Data Source" + ], + "ToolShed id": "art", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/art", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/art", + "Galaxy wrapper version": "2014.11.03.0", + "Conda id": "art", + "Conda version": "2016.06.05", + "EDAM operation (no superclasses)": [ + "Conversion" + ], + "EDAM topic (no superclasses)": [ + "Bioinformatics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "artic", + "Galaxy tool ids": [ + "artic_guppyplex", + "artic_minion" + ], + "Description": "The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building", + "bio.tool id": "artic", + "bio.tool ids": [ + "artic" + ], + "biii": null, + "bio.tool name": "ARTIC", + "bio.tool description": "A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/artic-network/fieldbioinformatics", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic", + "Galaxy wrapper version": null, + "Conda id": "artic", + "Conda version": "1.2.4", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "assembly-stats", + "Galaxy tool ids": [ + "assembly_stats" + ], + "Description": "Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/rjchallis/assembly-stats", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "assembly_stats", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats", + "Galaxy wrapper version": "17.02", + "Conda id": "rjchallis-assembly-stats", + "Conda version": "17.02", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "augustus", + "Galaxy tool ids": [ + "augustus", + "augustus_training" + ], + "Description": "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.", + "bio.tool id": "augustus", + "bio.tool ids": [ + "augustus" + ], + "biii": null, + "bio.tool name": "AUGUSTUS", + "bio.tool description": "AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.", + "EDAM operation": [ + "Gene prediction", + "Ab-initio gene prediction", + "Homology-based gene prediction", + "Homology-based gene prediction", + "Operation" + ], + "EDAM topic": [ + "Gene transcripts", + "Gene and protein families" + ], + "Status": "To update", + "Source": "http://bioinf.uni-greifswald.de/augustus/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "augustus", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus", + "Galaxy wrapper version": "3.4.0", + "Conda id": "augustus", + "Conda version": "3.5.0", + "EDAM operation (no superclasses)": [ + "Ab-initio gene prediction", + "Homology-based gene prediction", + "Homology-based gene prediction", + "Operation" + ], + "EDAM topic (no superclasses)": [ + "Gene transcripts", + "Gene and protein families" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "b2btools", + "Galaxy tool ids": [ + "b2btools_single_sequence" + ], + "Description": "This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.", + "bio.tool id": "b2btools", + "bio.tool ids": [ + "b2btools" + ], + "biii": null, + "bio.tool name": "b2bTools", + "bio.tool description": "The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA", + "EDAM operation": [ + "Protein disorder prediction", + "Protein secondary structure prediction", + "Protein feature detection" + ], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bio2byte.be", + "ToolShed categories": [ + "Computational chemistry", + "Molecular Dynamics", + "Proteomics", + "Sequence Analysis", + "Synthetic Biology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools", + "Galaxy wrapper version": "3.0.5+galaxy0", + "Conda id": "b2btools", + "Conda version": "3.0.6", + "EDAM operation (no superclasses)": [ + "Protein disorder prediction", + "Protein secondary structure prediction" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bakta", + "Galaxy tool ids": [ + "bakta" + ], + "Description": "\"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.\"", + "bio.tool id": "bakta", + "bio.tool ids": [ + "bakta" + ], + "biii": null, + "bio.tool name": "Bakta", + "bio.tool description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Genomics", + "Data submission, annotation and curation", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/oschwengers/bakta", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bakta", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta", + "Galaxy wrapper version": "1.9.3", + "Conda id": "bakta", + "Conda version": "1.9.3", + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Data submission, annotation and curation", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bam_to_scidx", + "Galaxy tool ids": [ + "bam_to_scidx" + ], + "Description": "Contains a tool that converts a BAM file to an ScIdx file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "bam_to_scidx", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx", + "Galaxy wrapper version": "1.0.1", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bamutil", + "Galaxy tool ids": [ + "bamutil_clip_overlap", + "bamutil_diff" + ], + "Description": "bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/statgen/bamUtil", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bamutil", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil", + "Galaxy wrapper version": null, + "Conda id": "bamutil", + "Conda version": "1.0.15", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bandage", + "Galaxy tool ids": [ + "bandage_image", + "bandage_info" + ], + "Description": "Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily", + "bio.tool id": "bandage", + "bio.tool ids": [ + "bandage" + ], + "biii": null, + "bio.tool name": "Bandage", + "bio.tool description": "GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.", + "EDAM operation": [ + "Sequence assembly visualisation" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/rrwick/Bandage", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "bandage", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage", + "Galaxy wrapper version": "2022.09", + "Conda id": "bandage_ng", + "Conda version": "2022.09", + "EDAM operation (no superclasses)": [ + "Sequence assembly visualisation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "barcode_splitter", + "Galaxy tool ids": [ + "barcode_splitter" + ], + "Description": "A utility to split sequence files using multiple sets of barcodes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/princeton_genomics/barcode_splitter/", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "barcode_splitter", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter", + "Galaxy wrapper version": "0.18.4.0", + "Conda id": "barcode_splitter", + "Conda version": "0.18.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "baredsc", + "Galaxy tool ids": [ + "baredsc_1d", + "baredsc_2d", + "baredsc_combine_1d", + "baredsc_combine_2d" + ], + "Description": "baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.", + "bio.tool id": "baredsc", + "bio.tool ids": [ + "baredsc" + ], + "biii": null, + "bio.tool name": "baredSC", + "bio.tool description": "The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.", + "EDAM operation": [ + "Data retrieval", + "Expression correlation analysis", + "Differential gene expression profiling" + ], + "EDAM topic": [ + "RNA-Seq", + "Cytometry", + "Transcriptomics", + "Gene transcripts", + "Statistics and probability" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lldelisle/baredSC", + "ToolShed categories": [ + "Transcriptomics", + "Visualization" + ], + "ToolShed id": "baredsc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc", + "Galaxy wrapper version": "1.1.3", + "Conda id": "baredsc", + "Conda version": "1.1.3", + "EDAM operation (no superclasses)": [ + "Data retrieval", + "Expression correlation analysis", + "Differential gene expression profiling" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Cytometry", + "Transcriptomics", + "Gene transcripts", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "barrnap", + "Galaxy tool ids": [ + "barrnap" + ], + "Description": "Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.", + "bio.tool id": "barrnap", + "bio.tool ids": [ + "barrnap" + ], + "biii": null, + "bio.tool name": "Barrnap", + "bio.tool description": "Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).", + "EDAM operation": [ + "Gene prediction" + ], + "EDAM topic": [ + "Genomics", + "Model organisms", + "Model organisms" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "barrnap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap", + "Galaxy wrapper version": "1.2.2", + "Conda id": "barrnap", + "Conda version": "0.9", + "EDAM operation (no superclasses)": [ + "Gene prediction" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Model organisms", + "Model organisms" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "basil", + "Galaxy tool ids": [ + "basil" + ], + "Description": "Breakpoint detection, including large insertions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/seqan/anise_basil", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "basil", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil", + "Galaxy wrapper version": "1.2.0", + "Conda id": "anise_basil", + "Conda version": "1.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bax2bam", + "Galaxy tool ids": [ + "bax2bam" + ], + "Description": "BAX to BAM converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/pacificbiosciences/bax2bam/", + "ToolShed categories": [ + "Convert Formats", + "Sequence Analysis" + ], + "ToolShed id": "bax2bam", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam", + "Galaxy wrapper version": "0.0.11", + "Conda id": "bax2bam", + "Conda version": "0.0.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bayescan", + "Galaxy tool ids": [ + "BayeScan" + ], + "Description": "Detecting natural selection from population-based genetic data", + "bio.tool id": "bayescan", + "bio.tool ids": [ + "bayescan" + ], + "biii": null, + "bio.tool name": "BayeScan", + "bio.tool description": "BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.", + "EDAM operation": [ + "Statistical inference" + ], + "EDAM topic": [ + "Genetics", + "Evolutionary biology", + "Statistics and probability", + "DNA polymorphism" + ], + "Status": "To update", + "Source": "http://cmpg.unibe.ch/software/BayeScan/index.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bayescan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan", + "Galaxy wrapper version": "2.1", + "Conda id": "bayescan", + "Conda version": "2.0.1", + "EDAM operation (no superclasses)": [ + "Statistical inference" + ], + "EDAM topic (no superclasses)": [ + "Genetics", + "Evolutionary biology", + "Statistics and probability", + "DNA polymorphism" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bbtools", + "Galaxy tool ids": [ + "bbtools_bbduk", + "bbtools_bbmap", + "bbtools_bbmerge", + "bbtools_bbnorm", + "bbtools_callvariants", + "bbtools_tadpole" + ], + "Description": "BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.", + "bio.tool id": "bbmap", + "bio.tool ids": [ + "bbtools", + "bbmap" + ], + "biii": null, + "bio.tool name": "BBMap", + "bio.tool description": "BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.", + "EDAM operation": [ + "RNA-Seq analysis", + "Sequence trimming", + "Read mapping", + "Sequence contamination filtering", + "Read binning", + "Sequence alignment" + ], + "EDAM topic": [ + "Sequencing", + "RNA splicing", + "Whole genome sequencing", + "Phylogenetics", + "Metagenomics", + "RNA-Seq" + ], + "Status": "Up-to-date", + "Source": "https://jgi.doe.gov/data-and-tools/bbtools/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bbtools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools", + "Galaxy wrapper version": "39.06", + "Conda id": "bbmap", + "Conda version": "39.06", + "EDAM operation (no superclasses)": [ + "RNA-Seq analysis", + "Sequence trimming", + "Read mapping", + "Sequence contamination filtering", + "Read binning", + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "RNA splicing", + "Whole genome sequencing", + "Phylogenetics", + "Metagenomics", + "RNA-Seq" + ], + "Available on UseGalaxy.org": 6, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bcftools", + "Galaxy tool ids": [ + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@_from_vcf", + "bcftools_@EXECUTABLE@_to_vcf", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_plugin_@PLUGIN_ID@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@_list_samples", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@", + "bcftools_@EXECUTABLE@" + ], + "Description": "BCFtools toolkit wrappers", + "bio.tool id": "bcftools", + "bio.tool ids": [ + "bcftools" + ], + "biii": null, + "bio.tool name": "BCFtools", + "bio.tool description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.", + "EDAM operation": [ + "Data handling", + "Variant calling" + ], + "EDAM topic": [ + "Genetic variation", + "DNA polymorphism", + "GWAS study", + "Genotyping experiment" + ], + "Status": "To update", + "Source": "https://samtools.github.io/bcftools/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools", + "Galaxy wrapper version": "1.15.1", + "Conda id": "bcftools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [ + "Data handling", + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "DNA polymorphism", + "GWAS study", + "Genotyping experiment" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bctools", + "Galaxy tool ids": [ + "bctools_convert_to_binary_barcode", + "bctools_extract_crosslinked_nucleotides", + "bctools_extract_alignment_ends", + "bctools_extract_barcodes", + "bctools_merge_pcr_duplicates", + "bctools_remove_tail", + "bctools_remove_spurious_events" + ], + "Description": "bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/dmaticzka/bctools", + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools", + "Galaxy wrapper version": "0.2.2", + "Conda id": "bctools", + "Conda version": "0.2.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "beacon2", + "Galaxy tool ids": [ + "beacon2_csv2xlsx", + "beacon2_pxf2bff", + "beacon2_vcf2bff" + ], + "Description": "beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).", + "bio.tool id": "ga4gh_beacon", + "bio.tool ids": [ + "ga4gh_beacon" + ], + "biii": null, + "bio.tool name": "GA4GH Beacon", + "bio.tool description": "A global search engine for genetic mutations.", + "EDAM operation": [ + "Service discovery", + "Database search", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Genetic variation", + "Population genetics", + "Data security", + "Rare diseases" + ], + "Status": "Up-to-date", + "Source": "https://github.com/EGA-archive/beacon2-ri-tools/tree/main", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "beacon2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2", + "Galaxy wrapper version": "2.0.0", + "Conda id": "beacon2-ri-tools", + "Conda version": "2.0.0", + "EDAM operation (no superclasses)": [ + "Service discovery", + "Database search", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Genetic variation", + "Population genetics", + "Data security", + "Rare diseases" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "beagle", + "Galaxy tool ids": [ + "beagle" + ], + "Description": "Beagle is a program for phasing and imputing missing genotypes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://faculty.washington.edu/browning/beagle/beagle.html", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "beagle", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle", + "Galaxy wrapper version": "5.2_21Apr21.304", + "Conda id": "beagle", + "Conda version": "5.4_22Jul22.46e", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bedops", + "Galaxy tool ids": [ + "bedops-sort-bed" + ], + "Description": "BEDOPS: high-performance genomic feature operations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://bedops.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "bedops_sortbed", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://bedops.readthedocs.io/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops", + "Galaxy wrapper version": "2.4.41", + "Conda id": "bedops", + "Conda version": "2.4.41", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bedtools", + "Galaxy tool ids": [ + "bedtools_annotatebed", + "bedtools_bamtobed", + "bedtools_bed12tobed6", + "bedtools_bedtobam", + "bedtools_bedtoigv", + "bedtools_bedpetobam", + "bedtools_closestbed", + "bedtools_clusterbed", + "bedtools_complementbed", + "bedtools_coveragebed", + "bedtools_expandbed", + "bedtools_fisher", + "bedtools_flankbed", + "bedtools_genomecoveragebed", + "bedtools_getfastabed", + "bedtools_groupbybed", + "bedtools_intersectbed", + "bedtools_jaccard", + "bedtools_links", + "bedtools_makewindowsbed", + "bedtools_map", + "bedtools_maskfastabed", + "bedtools_mergebed", + "bedtools_multicovtbed", + "bedtools_multiintersectbed", + "bedtools_nucbed", + "bedtools_overlapbed", + "bedtools_randombed", + "bedtools_reldistbed", + "bedtools_shufflebed", + "bedtools_slopbed", + "bedtools_sortbed", + "bedtools_spacingbed", + "bedtools_subtractbed", + "bedtools_tagbed", + "bedtools_unionbedgraph", + "bedtools_windowbed" + ], + "Description": "bedtools is a powerful toolset for genome arithmetic", + "bio.tool id": "bedtools", + "bio.tool ids": [ + "bedtools" + ], + "biii": null, + "bio.tool name": "BEDTools", + "bio.tool description": "BEDTools is an extensive suite of utilities for comparing genomic features in BED format.", + "EDAM operation": [ + "Mapping" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/arq5x/bedtools2", + "ToolShed categories": [ + "Genomic Interval Operations", + "Text Manipulation" + ], + "ToolShed id": "bedtools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools", + "Galaxy wrapper version": "2.31.1", + "Conda id": "bedtools", + "Conda version": "2.31.1", + "EDAM operation (no superclasses)": [ + "Mapping" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 37, + "Available on UseGalaxy.org.au": 37, + "Available on UseGalaxy.eu": 37, + "Available on UseGalaxy.org.fr": 37 + }, + { + "Galaxy wrapper id": "bellerophon", + "Galaxy tool ids": [ + "bellerophon" + ], + "Description": "Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/davebx/bellerophon", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bellerophon", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/davebx/bellerophon", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon", + "Galaxy wrapper version": "1.0", + "Conda id": "bellerophon", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "berokka", + "Galaxy tool ids": [ + "berokka" + ], + "Description": "Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/berokka", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "berokka", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka", + "Galaxy wrapper version": "0.2.3", + "Conda id": "berokka", + "Conda version": "0.2.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bigscape", + "Galaxy tool ids": [ + "bigscape" + ], + "Description": "Construct sequence similarity networks of BGCs and groups them into GCF", + "bio.tool id": "BiG-SCAPE", + "bio.tool ids": [ + "BiG-SCAPE" + ], + "biii": null, + "bio.tool name": "BiG-SCAPE", + "bio.tool description": "A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.", + "EDAM operation": [ + "Clustering", + "Global alignment", + "Fold recognition" + ], + "EDAM topic": [ + "Phylogeny", + "Microbial ecology", + "Mapping", + "Metabolomics", + "Bioinformatics", + "Gene and protein families" + ], + "Status": "Up-to-date", + "Source": "https://github.com/medema-group/BiG-SCAPE", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "bigscape", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape", + "Galaxy wrapper version": "1.1.9", + "Conda id": "bigscape", + "Conda version": "1.1.9", + "EDAM operation (no superclasses)": [ + "Clustering", + "Global alignment", + "Fold recognition" + ], + "EDAM topic (no superclasses)": [ + "Phylogeny", + "Microbial ecology", + "Mapping", + "Metabolomics", + "Bioinformatics", + "Gene and protein families" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "binning_refiner", + "Galaxy tool ids": [ + "bin_refiner" + ], + "Description": "Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.", + "bio.tool id": "binning_refiner", + "bio.tool ids": [ + "binning_refiner" + ], + "biii": null, + "bio.tool name": "Binning_refiner", + "bio.tool description": "Improving genome bins through the combination of different binning programs", + "EDAM operation": [ + "Read binning", + "Sequence clustering" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence assembly", + "Microbial ecology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/songweizhi/Binning_refiner", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "binning_refiner", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner", + "Galaxy wrapper version": "1.4.3", + "Conda id": "binning_refiner", + "Conda version": "1.4.3", + "EDAM operation (no superclasses)": [ + "Read binning", + "Sequence clustering" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence assembly", + "Microbial ecology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bioext", + "Galaxy tool ids": [ + "bioext_bam2msa", + "bioext_bealign" + ], + "Description": "A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pypi.python.org/pypi/biopython-extensions/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/davebx/bioext-gx/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext", + "Galaxy wrapper version": "0.21.2", + "Conda id": "python-bioext", + "Conda version": "0.21.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bioinformatics_cafe", + "Galaxy tool ids": [ + "fasta_regex_finder" + ], + "Description": "Miscellanea of scripts for bioinformatics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/dariober/bioinformatics-cafe/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bioinformatics_cafe", + "Galaxy wrapper owner": "mbernt", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe", + "Galaxy wrapper version": "0.1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "biom_format", + "Galaxy tool ids": [ + "biom_add_metadata", + "biom_convert", + "biom_from_uc", + "biom_normalize_table", + "biom_subset_table", + "biom_summarize_table" + ], + "Description": "The biom-format package provides a command line interface and Python API for working with BIOM files.", + "bio.tool id": "biomformat", + "bio.tool ids": [ + "biomformat" + ], + "biii": null, + "bio.tool name": "biomformat", + "bio.tool description": "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly \"R flavor\" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.", + "EDAM operation": [ + "Formatting" + ], + "EDAM topic": [ + "Laboratory information management", + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/biocore/biom-format", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format", + "Galaxy wrapper version": "2.1.15", + "Conda id": "biom-format", + "Conda version": "2.1.7", + "EDAM operation (no superclasses)": [ + "Formatting" + ], + "EDAM topic (no superclasses)": [ + "Laboratory information management", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bioperl", + "Galaxy tool ids": [ + "bp_genbank2gff3" + ], + "Description": "Converts GenBank format files to GFF3", + "bio.tool id": "bioperl", + "bio.tool ids": [ + "bioperl" + ], + "biii": null, + "bio.tool name": "BioPerl", + "bio.tool description": "A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.", + "EDAM operation": [ + "Data handling", + "Service invocation" + ], + "EDAM topic": [ + "Genomics", + "Software engineering", + "Data management" + ], + "Status": "To update", + "Source": "https://bioperl.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bp_genbank2gff3", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl", + "Galaxy wrapper version": "1.1", + "Conda id": "perl-bioperl", + "Conda version": "1.7.8", + "EDAM operation (no superclasses)": [ + "Data handling", + "Service invocation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Software engineering" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "biscot", + "Galaxy tool ids": [ + "biscot" + ], + "Description": "Bionano scaffolding correction tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/institut-de-genomique/biscot", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "biscot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/bgruening/iuc/tree/master/tools/biscot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot", + "Galaxy wrapper version": "2.3.3", + "Conda id": "biscot", + "Conda version": "2.3.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast", + "Galaxy tool ids": [ + "magicblast" + ], + "Description": "Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://ncbi.github.io/magicblast/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "magicblast", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast", + "Galaxy wrapper version": "1.7.0", + "Conda id": "magicblast", + "Conda version": "1.7.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blastxml_to_gapped_gff3", + "Galaxy tool ids": [ + "blastxml_to_gapped_gff3" + ], + "Description": "BlastXML to gapped GFF3", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats", + "Sequence Analysis" + ], + "ToolShed id": "blastxml_to_gapped_gff3", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3", + "Galaxy wrapper version": "1.1", + "Conda id": "bcbiogff", + "Conda version": "0.6.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bowtie2", + "Galaxy tool ids": [ + "bowtie2" + ], + "Description": "Bowtie2: Fast and sensitive read alignment", + "bio.tool id": "bowtie2", + "bio.tool ids": [ + "bowtie2" + ], + "biii": null, + "bio.tool name": "Bowtie 2", + "bio.tool description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.", + "EDAM operation": [ + "Read mapping" + ], + "EDAM topic": [ + "Mapping", + "Genomics", + "Mapping" + ], + "Status": "To update", + "Source": "http://bowtie-bio.sourceforge.net/bowtie2", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "bowtie2", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2", + "Galaxy wrapper version": "2.5.3", + "Conda id": "bowtie2", + "Conda version": "2.5.4", + "EDAM operation (no superclasses)": [ + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Mapping", + "Genomics", + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bracken", + "Galaxy tool ids": [ + "est_abundance" + ], + "Description": "Bayesian Reestimation of Abundance with KrakEN", + "bio.tool id": "bracken", + "bio.tool ids": [ + "bracken" + ], + "biii": null, + "bio.tool name": "Bracken", + "bio.tool description": "Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.", + "EDAM operation": [ + "Statistical calculation" + ], + "EDAM topic": [ + "Metagenomics", + "Microbial ecology" + ], + "Status": "Up-to-date", + "Source": "https://ccb.jhu.edu/software/bracken/", + "ToolShed categories": [ + "Sequence Analysis", + "Metagenomics" + ], + "ToolShed id": "bracken", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken", + "Galaxy wrapper version": "2.9", + "Conda id": "bracken", + "Conda version": "2.9", + "EDAM operation (no superclasses)": [ + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbial ecology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "breseq", + "Galaxy tool ids": [ + "breseq" + ], + "Description": "Predicts mutations in microbial genomes", + "bio.tool id": "breseq", + "bio.tool ids": [ + "breseq" + ], + "biii": null, + "bio.tool name": "breseq", + "bio.tool description": "Runs Breseq software on a set of fastq files.", + "EDAM operation": [ + "Polymorphism detection" + ], + "EDAM topic": [ + "Sequencing", + "Sequence analysis", + "DNA mutation" + ], + "Status": "To update", + "Source": "https://github.com/barricklab/breseq", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "breseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq", + "Galaxy wrapper version": "0.35.5", + "Conda id": "breseq", + "Conda version": "0.38.3", + "EDAM operation (no superclasses)": [ + "Polymorphism detection" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence analysis", + "DNA mutation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "busco", + "Galaxy tool ids": [ + "busco" + ], + "Description": "BUSCO assess genome and annotation completeness", + "bio.tool id": "busco", + "bio.tool ids": [ + "busco" + ], + "biii": null, + "bio.tool name": "BUSCO", + "bio.tool description": "Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", + "EDAM operation": [ + "Sequence assembly validation", + "Scaffolding", + "Genome assembly", + "Transcriptome assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Genomics", + "Transcriptomics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://gitlab.com/ezlab/busco/-/releases", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "busco", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco", + "Galaxy wrapper version": "5.5.0", + "Conda id": "busco", + "Conda version": "5.7.1", + "EDAM operation (no superclasses)": [ + "Sequence assembly validation", + "Scaffolding", + "Genome assembly", + "Transcriptome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Transcriptomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bwa", + "Galaxy tool ids": [ + "bwa_mem", + "bwa" + ], + "Description": "Wrapper for bwa mem, aln, sampe, and samse", + "bio.tool id": "bwa", + "bio.tool ids": [ + "bwa" + ], + "biii": null, + "bio.tool name": "BWA", + "bio.tool description": "Fast, accurate, memory-efficient aligner for short and long sequencing reads", + "EDAM operation": [ + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Sequence alignment", + "Generation", + "Sequence alignment", + "Generation", + "Sequence alignment", + "Sequence alignment" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "http://bio-bwa.sourceforge.net/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "bwa", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa", + "Galaxy wrapper version": "0.7.18", + "Conda id": "bwa", + "Conda version": "0.7.18", + "EDAM operation (no superclasses)": [ + "Genome indexing", + "Sequence alignment", + "Read mapping", + "Sequence alignment", + "Generation", + "Sequence alignment", + "Generation", + "Sequence alignment", + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "bwa_mem2", + "Galaxy tool ids": [ + "bwa_mem2" + ], + "Description": "Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.", + "bio.tool id": "bwa-mem2", + "bio.tool ids": [ + "bwa-mem2" + ], + "biii": null, + "bio.tool name": "Bwa-mem2", + "bio.tool description": "Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/bwa-mem2/bwa-mem2", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "bwa_mem2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2", + "Galaxy wrapper version": "2.2.1", + "Conda id": "bwa-mem2", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bwameth", + "Galaxy tool ids": [ + "bwameth" + ], + "Description": "Fast and accurate alignment of BS-seq reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/brentp/bwa-meth", + "ToolShed categories": [ + "Sequence Analysis", + "Next Gen Mappers" + ], + "ToolShed id": "bwameth", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth", + "Galaxy wrapper version": "0.2.7", + "Conda id": "bwameth", + "Conda version": "0.2.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cactus", + "Galaxy tool ids": [ + "cactus_cactus", + "cactus_export" + ], + "Description": "Cactus is a reference-free whole-genome multiple alignment program", + "bio.tool id": "cactus", + "bio.tool ids": [ + "cactus" + ], + "biii": null, + "bio.tool name": "Cactus", + "bio.tool description": "Cactus is a reference-free whole-genome multiple alignment program.", + "EDAM operation": [ + "Multiple sequence alignment", + "Genome alignment" + ], + "EDAM topic": [ + "Genomics", + "Sequence analysis", + "Phylogeny", + "Sequence assembly", + "Mapping", + "Phylogenetics" + ], + "Status": "To update", + "Source": "https://github.com/ComparativeGenomicsToolkit/cactus", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "cactus", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus", + "Galaxy wrapper version": "2.7.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Multiple sequence alignment", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly", + "Mapping", + "Phylogenetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "calculate_contrast_threshold", + "Galaxy tool ids": [ + "calculate_contrast_threshold" + ], + "Description": "Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold", + "ToolShed categories": [ + "Visualization", + "Genomic Interval Operations", + "SAM" + ], + "ToolShed id": "calculate_contrast_threshold", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold", + "Galaxy wrapper version": "1.0.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "calculate_numeric_param", + "Galaxy tool ids": [ + "calculate_numeric_param" + ], + "Description": "Calculate a numeric parameter value using integer and float values.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "calculate_numeric_param", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param", + "Galaxy wrapper version": "0.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cami_amber", + "Galaxy tool ids": [ + "cami_amber", + "cami_amber_add", + "cami_amber_convert" + ], + "Description": "Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/CAMI-challenge/AMBER", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "cami_amber", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber", + "Galaxy wrapper version": "2.0.4", + "Conda id": "cami-amber", + "Conda version": "2.0.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cat", + "Galaxy tool ids": [ + "cat_add_names", + "cat_bins", + "cat_contigs", + "cat_prepare", + "cat_summarise" + ], + "Description": "Contig Annotation Tool (CAT)", + "bio.tool id": "cat_bins", + "bio.tool ids": [ + "cat_bins" + ], + "biii": null, + "bio.tool name": "CAT and BAT", + "bio.tool description": "Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.", + "EDAM operation": [ + "Taxonomic classification", + "Sequence assembly", + "Coding region prediction" + ], + "EDAM topic": [ + "Metagenomics", + "Metagenomic sequencing", + "Taxonomy", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/dutilh/CAT", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "contig_annotation_tool", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat", + "Galaxy wrapper version": "5.2.3", + "Conda id": "cat", + "Conda version": "5.3", + "EDAM operation (no superclasses)": [ + "Taxonomic classification", + "Sequence assembly", + "Coding region prediction" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Metagenomic sequencing", + "Taxonomy", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cdhit", + "Galaxy tool ids": [ + "cd_hit" + ], + "Description": "Cluster or compare biological sequence datasets", + "bio.tool id": "cd-hit", + "bio.tool ids": [ + "cd-hit" + ], + "biii": null, + "bio.tool name": "cd-hit", + "bio.tool description": "Cluster a nucleotide dataset into representative sequences.", + "EDAM operation": [ + "Sequence clustering" + ], + "EDAM topic": [ + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "http://weizhongli-lab.org/cd-hit/", + "ToolShed categories": [ + "Sequence Analysis", + "Fasta Manipulation" + ], + "ToolShed id": "cd_hit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit", + "Galaxy wrapper version": "4.8.1", + "Conda id": "cd-hit", + "Conda version": "4.8.1", + "EDAM operation (no superclasses)": [ + "Sequence clustering" + ], + "EDAM topic (no superclasses)": [ + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cemitool", + "Galaxy tool ids": [ + "cemitool" + ], + "Description": "Gene co-expression network analysis tool", + "bio.tool id": "cemitool", + "bio.tool ids": [ + "cemitool" + ], + "biii": null, + "bio.tool name": "CEMiTool", + "bio.tool description": "It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.", + "EDAM operation": [ + "Enrichment analysis", + "Pathway or network analysis" + ], + "EDAM topic": [ + "Gene expression", + "Transcriptomics", + "Microarray experiment" + ], + "Status": "To update", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "cemitool", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool", + "Galaxy wrapper version": "1.18.1", + "Conda id": "bioconductor-cemitool", + "Conda version": "1.26.0", + "EDAM operation (no superclasses)": [ + "Enrichment analysis", + "Pathway or network analysis" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Microarray experiment" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "charts", + "Galaxy tool ids": [ + "charts" + ], + "Description": "Enables advanced visualization options in Galaxy Charts", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "charts", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts", + "Galaxy wrapper version": "1.0.1", + "Conda id": "r-getopt", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "checkm", + "Galaxy tool ids": [ + "checkm_analyze", + "checkm_lineage_set", + "checkm_lineage_wf", + "checkm_plot", + "checkm_qa", + "checkm_taxon_set", + "checkm_taxonomy_wf", + "checkm_tetra", + "checkm_tree", + "checkm_tree_qa" + ], + "Description": "Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes", + "bio.tool id": "checkm", + "bio.tool ids": [ + "checkm" + ], + "biii": null, + "bio.tool name": "CheckM", + "bio.tool description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.", + "EDAM operation": [ + "Sequence assembly validation", + "Validation", + "Sequence composition calculation", + "Sequencing quality control", + "Statistical calculation" + ], + "EDAM topic": [ + "Genomics", + "Phylogenomics", + "Phylogenetics", + "Taxonomy", + "Metagenomics", + "Data quality management" + ], + "Status": "To update", + "Source": "https://github.com/Ecogenomics/CheckM", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "checkm", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm", + "Galaxy wrapper version": "1.2.0", + "Conda id": "checkm-genome", + "Conda version": "1.2.2", + "EDAM operation (no superclasses)": [ + "Sequence assembly validation", + "Sequence composition calculation", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Phylogenomics", + "Phylogenetics", + "Taxonomy", + "Metagenomics", + "Data quality management" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.org.fr": 10 + }, + { + "Galaxy wrapper id": "cherri", + "Galaxy tool ids": [ + "cherri_eval", + "cherri_train" + ], + "Description": "Computational Help Evaluating RNA-RNA interactions", + "bio.tool id": "cherri", + "bio.tool ids": [ + "cherri" + ], + "biii": null, + "bio.tool name": "cherri", + "bio.tool description": "CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.", + "EDAM operation": [], + "EDAM topic": [ + "Molecular interactions, pathways and networks", + "Structure analysis", + "Machine learning" + ], + "Status": "To update", + "Source": "https://github.com/BackofenLab/Cherri", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri", + "Galaxy wrapper version": "0.7", + "Conda id": "cherri", + "Conda version": "0.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Molecular interactions, pathways and networks", + "Structure analysis", + "Machine learning" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "chewbbaca", + "Galaxy tool ids": [ + "chewbbaca_allelecall", + "chewbbaca_allelecallevaluator", + "chewbbaca_createschema", + "chewbbaca_downloadschema", + "chewbbaca_extractcgmlst", + "chewbbaca_joinprofiles", + "chewbbaca_nsstats", + "chewbbaca_prepexternalschema" + ], + "Description": "BSR-Based Allele Calling Algorithm", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/B-UMMI/chewBBACA/tree/master", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "chewbbaca", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca", + "Galaxy wrapper version": null, + "Conda id": "chewbbaca", + "Conda version": "3.3.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "chira", + "Galaxy tool ids": [ + "chira_collapse", + "chira_extract", + "chira_map", + "chira_merge", + "chira_quantify" + ], + "Description": "Chimeric Read Annotator for RNA-RNA interactome data", + "bio.tool id": "chira", + "bio.tool ids": [ + "chira" + ], + "biii": null, + "bio.tool name": "ChiRA", + "bio.tool description": "ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.", + "EDAM operation": [], + "EDAM topic": [ + "RNA", + "Molecular interactions, pathways and networks", + "Functional, regulatory and non-coding RNA" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pavanvidem/chira", + "ToolShed categories": [ + "RNA", + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "chira", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira", + "Galaxy wrapper version": "1.4.3", + "Conda id": "chira", + "Conda version": "1.4.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Molecular interactions, pathways and networks", + "Functional, regulatory and non-coding RNA" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "chopin2", + "Galaxy tool ids": [ + "chopin2" + ], + "Description": "Domain-Agnostic Supervised Learning with Hyperdimensional Computing", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/cumbof/chopin2", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "chopin2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2", + "Galaxy wrapper version": "1.0.8.post1", + "Conda id": "chopin2", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "chromeister", + "Galaxy tool ids": [ + "chromeister" + ], + "Description": "ultra-fast pairwise genome comparisons", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/estebanpw/chromeister", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "chromeister", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister", + "Galaxy wrapper version": "1.5.a", + "Conda id": "chromeister", + "Conda version": "1.5.a", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "circexplorer2", + "Galaxy tool ids": [ + "circexplorer2" + ], + "Description": "Comprehensive and integrative circular RNA analysis toolset.", + "bio.tool id": "circexplorer2", + "bio.tool ids": [ + "circexplorer2" + ], + "biii": null, + "bio.tool name": "CIRCexplorer2", + "bio.tool description": "Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.", + "EDAM operation": [], + "EDAM topic": [ + "RNA splicing", + "Gene transcripts", + "Literature and language" + ], + "Status": "Up-to-date", + "Source": "https://github.com/YangLab/CIRCexplorer2", + "ToolShed categories": [ + "RNA", + "Assembly" + ], + "ToolShed id": "circexplorer2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2", + "Galaxy wrapper version": "2.3.8", + "Conda id": "circexplorer2", + "Conda version": "2.3.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "RNA splicing", + "Gene transcripts", + "Literature and language" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "circos", + "Galaxy tool ids": [ + "circos_aln_to_links", + "circos_binlinks", + "circos_bundlelinks", + "circos", + "circos_gc_skew", + "circos_resample", + "circos_wiggle_to_scatter", + "circos_wiggle_to_stacked", + "circos_tableviewer", + "circos_interval_to_text", + "circos_interval_to_tile" + ], + "Description": "Build Circos Plots in Galaxy", + "bio.tool id": "galactic_circos", + "bio.tool ids": [ + "galactic_circos" + ], + "biii": null, + "bio.tool name": "Galactic Circos", + "bio.tool description": "Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.", + "EDAM operation": [ + "Sequence visualisation" + ], + "EDAM topic": [], + "Status": "To update", + "Source": "http://circos.ca/", + "ToolShed categories": [ + "Graphics" + ], + "ToolShed id": "circos", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos", + "Galaxy wrapper version": "0.69.8", + "Conda id": "circos", + "Conda version": "0.69.9", + "EDAM operation (no superclasses)": [ + "Sequence visualisation" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 11, + "Available on UseGalaxy.org.au": 11, + "Available on UseGalaxy.eu": 11, + "Available on UseGalaxy.org.fr": 11 + }, + { + "Galaxy wrapper id": "cite_seq_count", + "Galaxy tool ids": [ + "cite_seq_count" + ], + "Description": "Count CMO/HTO", + "bio.tool id": "CITE-seq-Count", + "bio.tool ids": [ + "CITE-seq-Count" + ], + "biii": null, + "bio.tool name": "CITE-seq-Count", + "bio.tool description": "Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.", + "EDAM operation": [ + "RNA-Seq quantification" + ], + "EDAM topic": [ + "Transcriptomics", + "Immunoproteins and antigens" + ], + "Status": "Up-to-date", + "Source": "https://github.com/Hoohm/CITE-seq-Count", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cite_seq_count", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count", + "Galaxy wrapper version": "1.4.4", + "Conda id": "cite-seq-count", + "Conda version": "1.4.4", + "EDAM operation (no superclasses)": [ + "RNA-Seq quantification" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Immunoproteins and antigens" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "clair3", + "Galaxy tool ids": [ + "clair3" + ], + "Description": "Symphonizing pileup and full-alignment for high-performance long-read variant calling", + "bio.tool id": "clair3", + "bio.tool ids": [ + "clair3" + ], + "biii": null, + "bio.tool name": "Clair3", + "bio.tool description": "Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.", + "EDAM operation": [ + "Variant calling" + ], + "EDAM topic": [ + "Molecular genetics" + ], + "Status": "To update", + "Source": "https://github.com/HKU-BAL/Clair3", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "clair3", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3", + "Galaxy wrapper version": "0.1.12", + "Conda id": "clair3", + "Conda version": "1.0.8", + "EDAM operation (no superclasses)": [ + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Molecular genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "clustalw", + "Galaxy tool ids": [ + "clustalw" + ], + "Description": "ClustalW multiple sequence alignment program for DNA or proteins", + "bio.tool id": "clustal2", + "bio.tool ids": [ + "clustal2" + ], + "biii": null, + "bio.tool name": "Clustal 2 (Clustal W, Clustal X)", + "bio.tool description": "Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.", + "EDAM operation": [ + "Multiple sequence alignment" + ], + "EDAM topic": [ + "Phylogeny", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "http://www.clustal.org/clustal2/", + "ToolShed categories": [ + "Phylogenetics", + "Sequence Analysis" + ], + "ToolShed id": "clustalw", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw", + "Galaxy wrapper version": "2.1", + "Conda id": "clustalw", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [ + "Multiple sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Phylogeny", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cnv-phenopacket", + "Galaxy tool ids": [ + "cnv_phenopacket" + ], + "Description": "cnv-phenopacket Converts TSV metadata file to JSON.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pypi.org/project/cnv-phenopacket/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "cnv_phenopacket", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket", + "Galaxy wrapper version": "1.0.2", + "Conda id": "cnv-phenopacket", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cnv-vcf2json", + "Galaxy tool ids": [ + "cnv_vcf2json" + ], + "Description": "cnv-vcf2json Converts structural variants VCF file to JSON.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pypi.org/project/cnv-phenopacket/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "cnv-vcf2json", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json", + "Galaxy wrapper version": "1.0.4", + "Conda id": "cnv-vcf2json", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cnvkit", + "Galaxy tool ids": [ + "cnvkit_access", + "cnvkit_antitarget", + "cnvkit_autobin", + "cnvkit_batch", + "cnvkit_breaks", + "cnvkit_call", + "cnvkit_coverage", + "cnvkit_diagram", + "cnvkit_fix", + "cnvkit_genemetrics", + "cnvkit_heatmap", + "cnvkit_reference", + "cnvkit_scatter", + "cnvkit_segment", + "cnvkit_segmetrics", + "cnvkit_sex", + "cnvkit_target" + ], + "Description": "detecting copy number variants and alterations genome-wide from high-throughput sequencing", + "bio.tool id": "cnvkit", + "bio.tool ids": [ + "cnvkit" + ], + "biii": null, + "bio.tool name": "CNVkit", + "bio.tool description": "CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.", + "EDAM operation": [ + "Variant calling" + ], + "EDAM topic": [ + "DNA structural variation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/etal/cnvkit", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "cnvkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit", + "Galaxy wrapper version": "0.9.11", + "Conda id": "cnvkit", + "Conda version": "0.9.11", + "EDAM operation (no superclasses)": [ + "Variant calling" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 17, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "codeml", + "Galaxy tool ids": [ + "codeml" + ], + "Description": "Detects positive selection", + "bio.tool id": "paml", + "bio.tool ids": [ + "paml" + ], + "biii": null, + "bio.tool name": "PAML", + "bio.tool description": "Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.", + "EDAM operation": [ + "Probabilistic sequence generation", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)", + "Phylogenetic tree analysis" + ], + "EDAM topic": [ + "Phylogenetics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://abacus.gene.ucl.ac.uk/software/paml.html", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "codeml", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml", + "Galaxy wrapper version": "4.9", + "Conda id": "paml", + "Conda version": "4.10.7", + "EDAM operation (no superclasses)": [ + "Probabilistic sequence generation" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cojac", + "Galaxy tool ids": [ + "cooc_mutbamscan", + "cooc_pubmut", + "cooc_tabmut" + ], + "Description": "co-occurrence of mutations on amplicons", + "bio.tool id": "cojac", + "bio.tool ids": [ + "cojac" + ], + "biii": null, + "bio.tool name": "COJAC", + "bio.tool description": "CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.", + "EDAM operation": [], + "EDAM topic": [ + "Genetic variation" + ], + "Status": "To update", + "Source": "https://github.com/cbg-ethz/cojac", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": "cojac", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac", + "Galaxy wrapper version": "0.9.1", + "Conda id": "cojac", + "Conda version": "0.9.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Genetic variation" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "colabfold", + "Galaxy tool ids": [ + "colabfold_alphafold", + "colabfold_msa" + ], + "Description": "Protein prediction based on AlphaFold2", + "bio.tool id": "Colabfold", + "bio.tool ids": [ + "Colabfold" + ], + "biii": null, + "bio.tool name": "ColabFold", + "bio.tool description": "ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.", + "EDAM operation": [ + "Database search", + "Protein structure prediction", + "Fold recognition" + ], + "EDAM topic": [ + "Protein folds and structural domains", + "Protein folding, stability and design", + "Structure prediction", + "Sequence sites, features and motifs", + "Metagenomics" + ], + "Status": "To update", + "Source": "https://github.com/sokrypton/ColabFold", + "ToolShed categories": [ + "Proteomics", + "Graphics" + ], + "ToolShed id": "colabfold", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/sokrypton/ColabFold", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold", + "Galaxy wrapper version": "1.5.5", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Database search", + "Protein structure prediction", + "Fold recognition" + ], + "EDAM topic (no superclasses)": [ + "Protein folds and structural domains", + "Protein folding, stability and design", + "Structure prediction", + "Sequence sites, features and motifs", + "Metagenomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "colibread", + "Galaxy tool ids": [ + "commet", + "discosnp_rad", + "discosnp_pp", + "kissplice", + "lordec", + "mapsembler2", + "takeabreak" + ], + "Description": "Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://colibread.inria.fr/", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "colibread", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread", + "Galaxy wrapper version": "24.7.14+galaxy0", + "Conda id": "commet", + "Conda version": "24.7.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "collection_column_join", + "Galaxy tool ids": [ + "collection_column_join" + ], + "Description": "Column Join on Collections", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "collection_column_join", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join", + "Galaxy wrapper version": "0.0.3", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "collection_element_identifiers", + "Galaxy tool ids": [ + "collection_element_identifiers" + ], + "Description": "Extract element identifiers of a collection", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "collection_element_identifiers", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers", + "Galaxy wrapper version": "0.0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "column_maker", + "Galaxy tool ids": [ + "Add_a_column1" + ], + "Description": "Compute an expression on every row", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "column_maker", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker", + "Galaxy wrapper version": "2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "column_order_header_sort", + "Galaxy tool ids": [ + "column_order_header_sort" + ], + "Description": "Sort Column Order by heading", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "column_order_header_sort", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort", + "Galaxy wrapper version": "0.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "column_remove_by_header", + "Galaxy tool ids": [ + "column_remove_by_header" + ], + "Description": "Remove columns by header", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "column_remove_by_header", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header", + "Galaxy wrapper version": "1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "compleasm", + "Galaxy tool ids": [ + "compleasm" + ], + "Description": "Compleasm: a faster and more accurate reimplementation of BUSCO", + "bio.tool id": "compleasm", + "bio.tool ids": [ + "compleasm" + ], + "biii": null, + "bio.tool name": "compleasm", + "bio.tool description": "\"Compleasm: a faster and more accurate reimplementation of BUSCO\"", + "EDAM operation": [ + "Sequence assembly validation", + "Sequence analysis", + "Scaffolding", + "Transcriptome assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Genomics", + "Transcriptomics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/huangnengCSU/compleasm", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "compleasm", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm", + "Galaxy wrapper version": "0.2.6", + "Conda id": "compleasm", + "Conda version": "0.2.6", + "EDAM operation (no superclasses)": [ + "Sequence assembly validation", + "Sequence analysis", + "Scaffolding", + "Transcriptome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Transcriptomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "compose_text_param", + "Galaxy tool ids": [ + "compose_text_param" + ], + "Description": "Compose a text parameter value using text, integer and float values", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "compose_text_param", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param", + "Galaxy wrapper version": "0.1.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "compress_file", + "Galaxy tool ids": [ + "compress_file" + ], + "Description": "Compress files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "compress_file", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file", + "Galaxy wrapper version": "0.1.0", + "Conda id": "gzip", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "concoct", + "Galaxy tool ids": [ + "concoct", + "concoct_coverage_table", + "concoct_cut_up_fasta", + "concoct_extract_fasta_bins", + "concoct_merge_cut_up_clustering" + ], + "Description": "CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.", + "bio.tool id": "concoct", + "bio.tool ids": [ + "concoct" + ], + "biii": null, + "bio.tool name": "CONCOCT", + "bio.tool description": "A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.", + "EDAM operation": [ + "Sequence clustering", + "Read binning" + ], + "EDAM topic": [ + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/BinPro/CONCOCT", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "concoct", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct", + "Galaxy wrapper version": "1.1.0", + "Conda id": "concoct", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [ + "Sequence clustering", + "Read binning" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "cosg", + "Galaxy tool ids": [ + "cosg" + ], + "Description": "Marker gene identification for single-cell sequencing data using COSG.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/genecell/COSG", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "cosg", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg", + "Galaxy wrapper version": "1.0.1", + "Conda id": "cosg", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "coverage_report", + "Galaxy tool ids": [ + "CoverageReport2" + ], + "Description": "Generate Detailed Coverage Report from BAM file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "coverage_report", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report", + "Galaxy wrapper version": "0.0.4", + "Conda id": "perl-number-format", + "Conda version": "1.76", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "coverm", + "Galaxy tool ids": [ + "coverm_contig", + "coverm_genome" + ], + "Description": "CoverM genome and contig wrappers", + "bio.tool id": "coverm", + "bio.tool ids": [ + "coverm" + ], + "biii": null, + "bio.tool name": "CoverM", + "bio.tool description": "Read coverage calculator for metagenomics", + "EDAM operation": [ + "Local alignment" + ], + "EDAM topic": [ + "Bioinformatics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/wwood/CoverM", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "coverm", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/coverm", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm", + "Galaxy wrapper version": "0.7.0", + "Conda id": "coverm", + "Conda version": "0.7.0", + "EDAM operation (no superclasses)": [ + "Local alignment" + ], + "EDAM topic (no superclasses)": [ + "Bioinformatics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "crispr_studio", + "Galaxy tool ids": [ + "crispr_studio" + ], + "Description": "CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.", + "bio.tool id": "crisprstudio", + "bio.tool ids": [ + "crisprstudio" + ], + "biii": null, + "bio.tool name": "CRISPRStudio", + "bio.tool description": "CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.", + "EDAM operation": [ + "Visualisation" + ], + "EDAM topic": [ + "Sequence analysis", + "Genomics", + "Data visualisation" + ], + "Status": "To update", + "Source": "https://github.com/moineaulab/CRISPRStudio", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "crispr_studio", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio", + "Galaxy wrapper version": "1+galaxy0", + "Conda id": "crispr_studio", + "Conda version": "1", + "EDAM operation (no superclasses)": [ + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Genomics", + "Data visualisation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "crosscontamination_barcode_filter", + "Galaxy tool ids": [ + "crosscontamination_barcode_filter" + ], + "Description": "Barcode contamination discovery tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "Visualization" + ], + "ToolShed id": "crosscontamination_barcode_filter", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter", + "Galaxy wrapper version": "0.3", + "Conda id": "r-ggplot2", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "crossmap", + "Galaxy tool ids": [ + "crossmap_bam", + "crossmap_bed", + "crossmap_bw", + "crossmap_gff", + "crossmap_region", + "crossmap_vcf", + "crossmap_wig" + ], + "Description": "CrossMap converts genome coordinates or annotation files between genome assemblies", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://crossmap.sourceforge.net/", + "ToolShed categories": [ + "Convert Formats", + "Genomic Interval Operations" + ], + "ToolShed id": "crossmap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap", + "Galaxy wrapper version": "0.6.1", + "Conda id": "crossmap", + "Conda version": "0.7.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cutadapt", + "Galaxy tool ids": [ + "cutadapt" + ], + "Description": "Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).", + "bio.tool id": "cutadapt", + "bio.tool ids": [ + "cutadapt" + ], + "biii": null, + "bio.tool name": "Cutadapt", + "bio.tool description": "Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.", + "EDAM operation": [ + "Sequence trimming", + "Primer removal", + "Read pre-processing" + ], + "EDAM topic": [ + "Genomics", + "Probes and primers", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://cutadapt.readthedocs.org/en/stable/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "cutadapt", + "Galaxy wrapper owner": "lparsons", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt", + "Galaxy wrapper version": "4.8", + "Conda id": "cutadapt", + "Conda version": "4.8", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "Primer removal", + "Read pre-processing" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Probes and primers", + "Sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cutesv", + "Galaxy tool ids": [ + "cutesv" + ], + "Description": "Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.", + "bio.tool id": "cuteSV", + "bio.tool ids": [ + "cuteSV" + ], + "biii": null, + "bio.tool name": "cuteSV", + "bio.tool description": "Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis", + "EDAM operation": [ + "Split read mapping", + "Genotyping", + "Structural variation detection" + ], + "EDAM topic": [ + "DNA structural variation", + "Sequencing", + "Computer science" + ], + "Status": "To update", + "Source": "https://github.com/tjiangHIT/cuteSV", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "cutesv", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv", + "Galaxy wrapper version": "1.0.8", + "Conda id": "cutesv", + "Conda version": "2.1.1", + "EDAM operation (no superclasses)": [ + "Split read mapping", + "Genotyping", + "Structural variation detection" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Computer science" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cwpair2", + "Galaxy tool ids": [ + "cwpair2" + ], + "Description": "Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "cwpair2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2", + "Galaxy wrapper version": "1.1.1", + "Conda id": "matplotlib", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dada2", + "Galaxy tool ids": [ + "dada2_assignTaxonomyAddspecies", + "dada2_dada", + "dada2_filterAndTrim", + "dada2_learnErrors", + "dada2_makeSequenceTable", + "dada2_mergePairs", + "dada2_plotComplexity", + "dada2_plotQualityProfile", + "dada2_removeBimeraDenovo", + "dada2_seqCounts" + ], + "Description": "DADA2 wrappers", + "bio.tool id": "dada2", + "bio.tool ids": [ + "dada2" + ], + "biii": null, + "bio.tool name": "dada2", + "bio.tool description": "This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.", + "EDAM operation": [ + "Variant calling", + "DNA barcoding" + ], + "EDAM topic": [ + "Sequencing", + "Genetic variation", + "Microbial ecology", + "Metagenomics" + ], + "Status": "To update", + "Source": "https://benjjneb.github.io/dada2/index.html", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "dada2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2", + "Galaxy wrapper version": null, + "Conda id": "bioconductor-dada2", + "Conda version": "1.30.0", + "EDAM operation (no superclasses)": [ + "Variant calling", + "DNA barcoding" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Genetic variation", + "Microbial ecology", + "Metagenomics" + ], + "Available on UseGalaxy.org": 10, + "Available on UseGalaxy.org.au": 10, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.org.fr": 10 + }, + { + "Galaxy wrapper id": "das_tool", + "Galaxy tool ids": [ + "Fasta_to_Contig2Bin", + "das_tool" + ], + "Description": "DAS Tool for genome resolved metagenomics", + "bio.tool id": "dastool", + "bio.tool ids": [ + "dastool" + ], + "biii": null, + "bio.tool name": "dastool", + "bio.tool description": "DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.", + "EDAM operation": [ + "Read binning" + ], + "EDAM topic": [ + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/cmks/DAS_Tool", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "das_tool", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool", + "Galaxy wrapper version": "1.1.7", + "Conda id": "das_tool", + "Conda version": "1.1.7", + "EDAM operation (no superclasses)": [ + "Read binning" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "data_source_iris_tcga", + "Galaxy tool ids": [ + "data_source_iris_tcga" + ], + "Description": "IRIS-TCGA Data source tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "data_source_iris_tcga", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga", + "Galaxy wrapper version": "1.0.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "datamash", + "Galaxy tool ids": [ + "datamash_ops", + "datamash_reverse", + "datamash_transpose" + ], + "Description": "GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.gnu.org/software/datamash/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash", + "Galaxy wrapper version": "1.8", + "Conda id": "datamash", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "decontaminator", + "Galaxy tool ids": [ + "decontaminator" + ], + "Description": "Deep Learning method for novel virus detection in sequencing data", + "bio.tool id": "decontaminator", + "bio.tool ids": [ + "decontaminator" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/cbib/decontaminator", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "decontaminator", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator", + "Galaxy wrapper version": "1.0.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "deepmicro", + "Galaxy tool ids": [ + "deepmicro" + ], + "Description": "Representation learning and classification framework", + "bio.tool id": "DeepMicro", + "bio.tool ids": [ + "DeepMicro" + ], + "biii": null, + "bio.tool name": "DeepMicro", + "bio.tool description": "Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.", + "EDAM operation": [ + "Essential dynamics", + "Splitting", + "Community profiling" + ], + "EDAM topic": [ + "Microbial ecology", + "Machine learning", + "Pathology", + "Public health and epidemiology", + "Allergy, clinical immunology and immunotherapeutics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/paulzierep/DeepMicro", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "deepmicro", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/paulzierep/DeepMicro", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro", + "Galaxy wrapper version": "1.4", + "Conda id": "deepmicro", + "Conda version": "1.4", + "EDAM operation (no superclasses)": [ + "Essential dynamics", + "Splitting" + ], + "EDAM topic (no superclasses)": [ + "Microbial ecology", + "Machine learning", + "Pathology", + "Public health and epidemiology", + "Allergy, clinical immunology and immunotherapeutics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "deepsig", + "Galaxy tool ids": [ + "deepsig" + ], + "Description": "Predictor of signal peptides in proteins based on deep learning", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/BolognaBiocomp/deepsig", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "deepsig", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig", + "Galaxy wrapper version": "1.2.5", + "Conda id": "deepsig", + "Conda version": "1.2.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "deepvariant", + "Galaxy tool ids": [ + "deepvariant" + ], + "Description": "DeepVariant is a deep learning-based variant caller", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/google/deepvariant", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "deepvariant", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant", + "Galaxy wrapper version": "1.5.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "deg_annotate", + "Galaxy tool ids": [ + "deg_annotate" + ], + "Description": "Annotate DESeq2/DEXSeq output tables", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "deg_annotate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate", + "Galaxy wrapper version": "1.1.0", + "Conda id": "bedtools", + "Conda version": "2.31.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "delly", + "Galaxy tool ids": [ + "delly_call", + "delly_classify", + "delly_cnv", + "delly_filter", + "delly_lr", + "delly_merge" + ], + "Description": "Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.", + "bio.tool id": "delly2", + "bio.tool ids": [ + "delly2" + ], + "biii": null, + "bio.tool name": "Delly2", + "bio.tool description": "Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.", + "EDAM operation": [ + "Indel detection", + "Structural variation detection", + "Variant calling", + "Genotyping", + "Genetic variation analysis" + ], + "EDAM topic": [ + "DNA structural variation", + "Sequencing", + "Pathology", + "Genomics", + "Genetic variation", + "Bioinformatics", + "Population genomics", + "Rare diseases" + ], + "Status": "To update", + "Source": "https://github.com/dellytools/delly", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "delly", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly", + "Galaxy wrapper version": "0.9.1", + "Conda id": "delly", + "Conda version": "1.2.6", + "EDAM operation (no superclasses)": [ + "Indel detection", + "Structural variation detection", + "Genotyping" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Genetic variation", + "Bioinformatics", + "Population genomics", + "Rare diseases" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "deseq2", + "Galaxy tool ids": [ + "deseq2" + ], + "Description": "Differential gene expression analysis based on the negative binomial distribution", + "bio.tool id": "DESeq2", + "bio.tool ids": [ + "DESeq2" + ], + "biii": null, + "bio.tool name": "DESeq2", + "bio.tool description": "R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.", + "EDAM operation": [ + "Differential gene expression analysis", + "RNA-Seq analysis" + ], + "EDAM topic": [ + "RNA-Seq" + ], + "Status": "To update", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "deseq2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2", + "Galaxy wrapper version": "2.11.40.8", + "Conda id": "bioconductor-deseq2", + "Conda version": "1.42.0", + "EDAM operation (no superclasses)": [ + "Differential gene expression analysis", + "RNA-Seq analysis" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "dexseq", + "Galaxy tool ids": [ + "dexseq", + "dexseq_count", + "plotdexseq" + ], + "Description": "Inference of differential exon usage in RNA-Seq", + "bio.tool id": "dexseq", + "bio.tool ids": [ + "dexseq" + ], + "biii": null, + "bio.tool name": "DEXSeq", + "bio.tool description": "The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.", + "EDAM operation": [ + "Enrichment analysis", + "Exonic splicing enhancer prediction" + ], + "EDAM topic": [ + "RNA-Seq" + ], + "Status": "Up-to-date", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "dexseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq", + "Galaxy wrapper version": "1.48.0", + "Conda id": "bioconductor-dexseq", + "Conda version": "1.48.0", + "EDAM operation (no superclasses)": [ + "Enrichment analysis", + "Exonic splicing enhancer prediction" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "diamond", + "Galaxy tool ids": [ + "bg_diamond", + "bg_diamond_makedb", + "bg_diamond_view" + ], + "Description": "DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.", + "bio.tool id": "diamond", + "bio.tool ids": [ + "diamond" + ], + "biii": null, + "bio.tool name": "Diamond", + "bio.tool description": "Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.", + "EDAM operation": [ + "Sequence alignment analysis" + ], + "EDAM topic": [ + "Sequence analysis", + "Proteins" + ], + "Status": "To update", + "Source": "https://github.com/bbuchfink/diamond", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "diamond", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond", + "Galaxy wrapper version": "2.0.15", + "Conda id": "diamond", + "Conda version": "2.1.9", + "EDAM operation (no superclasses)": [ + "Sequence alignment analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Proteins" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "diffbind", + "Galaxy tool ids": [ + "diffbind" + ], + "Description": "Diffbind provides functions for processing ChIP-Seq data.", + "bio.tool id": "diffbind", + "bio.tool ids": [ + "diffbind" + ], + "biii": null, + "bio.tool name": "DiffBind", + "bio.tool description": "Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.", + "EDAM operation": [ + "Differential binding analysis" + ], + "EDAM topic": [ + "ChIP-seq" + ], + "Status": "To update", + "Source": "http://bioconductor.org/packages/release/bioc/html/DiffBind.html", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "diffbind", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind", + "Galaxy wrapper version": "2.10.0", + "Conda id": "bioconductor-diffbind", + "Conda version": "3.12.0", + "EDAM operation (no superclasses)": [ + "Differential binding analysis" + ], + "EDAM topic (no superclasses)": [ + "ChIP-seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "dimet", + "Galaxy tool ids": [ + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@", + "dimet_@EXECUTABLE@" + ], + "Description": "DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/cbib/DIMet", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet", + "Galaxy wrapper version": "0.2.4", + "Conda id": "dimet", + "Conda version": "0.2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "disco", + "Galaxy tool ids": [ + "disco" + ], + "Description": "DISCO is a overlap-layout-consensus (OLC) metagenome assembler", + "bio.tool id": "disco", + "bio.tool ids": [ + "disco" + ], + "biii": null, + "bio.tool name": "DISCO", + "bio.tool description": "DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.", + "EDAM operation": [ + "Protein sequence analysis" + ], + "EDAM topic": [ + "Structure determination" + ], + "Status": "To update", + "Source": "http://disco.omicsbio.org/", + "ToolShed categories": [ + "Metagenomics", + "Assembly" + ], + "ToolShed id": "disco", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco", + "Galaxy wrapper version": null, + "Conda id": "disco", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [ + "Protein sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Structure determination" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dnabot", + "Galaxy tool ids": [ + "dnabot" + ], + "Description": "DNA assembly using BASIC on OpenTrons", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "dnabot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot", + "Galaxy wrapper version": "3.1.0", + "Conda id": "dnabot", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dnaweaver", + "Galaxy tool ids": [ + "dnaweaver" + ], + "Description": "Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/Edinburgh-Genome-Foundry/DnaWeaver", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "dnaweaver", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver", + "Galaxy wrapper version": "1.0.2", + "Conda id": "dnaweaver_synbiocad", + "Conda version": "1.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dram", + "Galaxy tool ids": [ + "dram_annotate", + "dram_distill", + "dram_merge_annotations", + "dram_neighborhoods", + "dram_strainer" + ], + "Description": "DRAM for distilling microbial metabolism to automate the curation of microbiome function", + "bio.tool id": "dram", + "bio.tool ids": [ + "dram" + ], + "biii": null, + "bio.tool name": "DRAM", + "bio.tool description": "Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes", + "EDAM operation": [ + "Gene functional annotation" + ], + "EDAM topic": [ + "Metagenomics", + "Biological databases", + "Molecular genetics" + ], + "Status": "To update", + "Source": "https://github.com/WrightonLabCSU/DRAM", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "dram", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram", + "Galaxy wrapper version": "1.3.5", + "Conda id": "dram", + "Conda version": "1.5.0", + "EDAM operation (no superclasses)": [ + "Gene functional annotation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Biological databases", + "Molecular genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "drep", + "Galaxy tool ids": [ + "drep_compare", + "drep_dereplicate" + ], + "Description": "dRep compares and dereplicates genome sets", + "bio.tool id": "drep", + "bio.tool ids": [ + "drep" + ], + "biii": null, + "bio.tool name": "dRep", + "bio.tool description": "Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.", + "EDAM operation": [ + "Genome comparison" + ], + "EDAM topic": [ + "Metagenomics", + "Genomics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/MrOlm/drep", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "drep", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep", + "Galaxy wrapper version": "3.5.0", + "Conda id": "drep", + "Conda version": "3.5.0", + "EDAM operation (no superclasses)": [ + "Genome comparison" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "dropletutils", + "Galaxy tool ids": [ + "dropletutils" + ], + "Description": "DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data", + "bio.tool id": "dropletutils", + "bio.tool ids": [ + "dropletutils" + ], + "biii": null, + "bio.tool name": "DropletUtils", + "bio.tool description": "Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.", + "EDAM operation": [ + "Loading", + "Community profiling" + ], + "EDAM topic": [ + "Gene expression", + "RNA-seq", + "Sequencing", + "Transcriptomics" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "dropletutils", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils", + "Galaxy wrapper version": "1.10.0", + "Conda id": "bioconductor-dropletutils", + "Conda version": "1.22.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Transcriptomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ebi_tools", + "Galaxy tool ids": [ + "ebi_metagenomics_run_downloader", + "ebi_search_rest_results" + ], + "Description": "Tools to query and download data from several EMBL-EBI databases", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.ebi.ac.uk/services/all", + "ToolShed categories": [ + "Web Services", + "Data Source" + ], + "ToolShed id": "ebi_tools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools", + "Galaxy wrapper version": "0.1.0", + "Conda id": "six", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "edger", + "Galaxy tool ids": [ + "edger" + ], + "Description": "Perform RNA-Seq differential expression analysis using edgeR pipeline", + "bio.tool id": "edger", + "bio.tool ids": [ + "edger" + ], + "biii": null, + "bio.tool name": "edgeR", + "bio.tool description": "Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.", + "EDAM operation": [ + "Differential gene expression analysis" + ], + "EDAM topic": [ + "Genetics", + "RNA-Seq", + "ChIP-seq" + ], + "Status": "To update", + "Source": "http://bioconductor.org/packages/release/bioc/html/edgeR.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "edger", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger", + "Galaxy wrapper version": "3.36.0", + "Conda id": "bioconductor-edger", + "Conda version": "4.0.16", + "EDAM operation (no superclasses)": [ + "Differential gene expression analysis" + ], + "EDAM topic (no superclasses)": [ + "Genetics", + "RNA-Seq", + "ChIP-seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "egsea", + "Galaxy tool ids": [ + "egsea" + ], + "Description": "This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing", + "bio.tool id": "egsea", + "bio.tool ids": [ + "egsea" + ], + "biii": null, + "bio.tool name": "EGSEA", + "bio.tool description": "This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.", + "EDAM operation": [ + "Gene set testing" + ], + "EDAM topic": [ + "Systems biology" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/EGSEA.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "egsea", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea", + "Galaxy wrapper version": "1.20.0", + "Conda id": "bioconductor-egsea", + "Conda version": "1.28.0", + "EDAM operation (no superclasses)": [ + "Gene set testing" + ], + "EDAM topic (no superclasses)": [ + "Systems biology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "emboss_5", + "Galaxy tool ids": [ + "EMBOSS: antigenic1", + "EMBOSS: backtranseq2", + "EMBOSS: banana3", + "EMBOSS: biosed4", + "EMBOSS: btwisted5", + "EMBOSS: cai6", + "EMBOSS: cai_custom6", + "EMBOSS: chaos7", + "EMBOSS: charge8", + "EMBOSS: checktrans9", + "EMBOSS: chips10", + "EMBOSS: cirdna11", + "EMBOSS: codcmp12", + "EMBOSS: coderet13", + "EMBOSS: compseq14", + "EMBOSS: cpgplot15", + "EMBOSS: cpgreport16", + "EMBOSS: cusp17", + "EMBOSS: cutseq18", + "EMBOSS: dan19", + "EMBOSS: degapseq20", + "EMBOSS: descseq21", + "EMBOSS: diffseq22", + "EMBOSS: digest23", + "EMBOSS: dotmatcher24", + "EMBOSS: dotpath25", + "EMBOSS: dottup26", + "EMBOSS: dreg27", + "EMBOSS: einverted28", + "EMBOSS: epestfind29", + "EMBOSS: equicktandem31", + "EMBOSS: est2genome32", + "EMBOSS: etandem33", + "EMBOSS: extractfeat34", + "EMBOSS: extractseq35", + "EMBOSS: freak36", + "EMBOSS: fuzznuc37", + "EMBOSS: fuzzpro38", + "EMBOSS: fuzztran39", + "EMBOSS: garnier40", + "EMBOSS: geecee41", + "EMBOSS: getorf42", + "EMBOSS: helixturnhelix43", + "EMBOSS: hmoment44", + "EMBOSS: iep45", + "EMBOSS: infoseq46", + "EMBOSS: isochore47", + "EMBOSS: lindna48", + "EMBOSS: marscan49", + "EMBOSS: maskfeat50", + "EMBOSS: maskseq51", + "EMBOSS: matcher52", + "EMBOSS: megamerger53", + "EMBOSS: merger54", + "EMBOSS: msbar55", + "EMBOSS: needle56", + "EMBOSS: newcpgreport57", + "EMBOSS: newcpgseek58", + "EMBOSS: newseq59", + "EMBOSS: noreturn60", + "EMBOSS: notseq61", + "EMBOSS: nthseq62", + "EMBOSS: octanol63", + "EMBOSS: oddcomp64", + "EMBOSS: palindrome65", + "EMBOSS: pasteseq66", + "EMBOSS: patmatdb67", + "EMBOSS: pepcoil68", + "EMBOSS: pepinfo69", + "EMBOSS: pepnet70", + "EMBOSS: pepstats71", + "EMBOSS: pepwheel72", + "EMBOSS: pepwindow73", + "EMBOSS: pepwindowall74", + "EMBOSS: plotcon75", + "EMBOSS: plotorf76", + "EMBOSS: polydot77", + "EMBOSS: preg78", + "EMBOSS: prettyplot79", + "EMBOSS: prettyseq80", + "EMBOSS: primersearch81", + "EMBOSS: revseq82", + "EMBOSS: seqmatchall83", + "EMBOSS: seqret84", + "EMBOSS: showfeat85", + "EMBOSS: shuffleseq87", + "EMBOSS: sigcleave88", + "EMBOSS: sirna89", + "EMBOSS: sixpack90", + "EMBOSS: skipseq91", + "EMBOSS: splitter92", + "EMBOSS: supermatcher95", + "EMBOSS: syco96", + "EMBOSS: tcode97", + "EMBOSS: textsearch98", + "EMBOSS: tmap99", + "EMBOSS: tranalign100", + "EMBOSS: transeq101", + "EMBOSS: trimest102", + "EMBOSS: trimseq103", + "EMBOSS: twofeat104", + "EMBOSS: union105", + "EMBOSS: vectorstrip106", + "EMBOSS: water107", + "EMBOSS: wobble108", + "EMBOSS: wordcount109", + "EMBOSS: wordmatch110" + ], + "Description": "Galaxy wrappers for EMBOSS version 5.0.0 tools", + "bio.tool id": "emboss", + "bio.tool ids": [ + "emboss" + ], + "biii": null, + "bio.tool name": "EMBOSS", + "bio.tool description": "Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.", + "EDAM operation": [ + "Sequence analysis", + "Local alignment", + "Sequence alignment analysis", + "Global alignment", + "Sequence alignment" + ], + "EDAM topic": [ + "Molecular biology", + "Sequence analysis", + "Biology" + ], + "Status": "To update", + "Source": "http://emboss.open-bio.org/", + "ToolShed categories": [ + "Sequence Analysis", + "Fasta Manipulation" + ], + "ToolShed id": "emboss_5", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5", + "Galaxy wrapper version": "5.0.0", + "Conda id": "emboss", + "Conda version": "6.6.0", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Local alignment", + "Sequence alignment analysis", + "Global alignment", + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Molecular biology", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 107, + "Available on UseGalaxy.org.au": 107, + "Available on UseGalaxy.eu": 107, + "Available on UseGalaxy.org.fr": 107 + }, + { + "Galaxy wrapper id": "ena_upload", + "Galaxy tool ids": [ + "ena_upload" + ], + "Description": "Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). ", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/usegalaxy-eu/ena-upload-cli", + "ToolShed categories": [ + "Data Export" + ], + "ToolShed id": "ena_upload", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload", + "Galaxy wrapper version": "0.7.1", + "Conda id": "ena-upload-cli", + "Conda version": "0.7.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "enasearch", + "Galaxy tool ids": [ + "enasearch_retrieve_analysis_report", + "enasearch_retrieve_data", + "enasearch_retrieve_run_report", + "enasearch_retrieve_taxons", + "enasearch_search_data" + ], + "Description": "A Python library for interacting with ENA's API", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/bebatut/enasearch", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "enasearch", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch", + "Galaxy wrapper version": null, + "Conda id": "enasearch", + "Conda version": "0.2.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ensembl_vep", + "Galaxy tool ids": [ + "ensembl_vep" + ], + "Description": "Ensembl VEP: Annotate VCFs with variant effect predictions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Ensembl/ensembl-vep", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "ensembl_vep", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep", + "Galaxy wrapper version": "110.1", + "Conda id": "ensembl-vep", + "Conda version": "112.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "episcanpy", + "Galaxy tool ids": [ + "episcanpy_build_matrix", + "episcanpy_cluster_embed", + "episcanpy_preprocess" + ], + "Description": "EpiScanpy – Epigenomics single cell analysis in python", + "bio.tool id": "episcanpy", + "bio.tool ids": [ + "episcanpy" + ], + "biii": null, + "bio.tool name": "epiScanpy", + "bio.tool description": "Epigenomics Single Cell Analysis in Python.", + "EDAM operation": [ + "Enrichment analysis", + "Imputation" + ], + "EDAM topic": [ + "Epigenomics", + "Cell biology", + "DNA" + ], + "Status": "To update", + "Source": "https://github.com/colomemaria/epiScanpy", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "episcanpy", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy", + "Galaxy wrapper version": "0.3.2", + "Conda id": "episcanpy", + "Conda version": "0.4.0", + "EDAM operation (no superclasses)": [ + "Enrichment analysis", + "Imputation" + ], + "EDAM topic (no superclasses)": [ + "Epigenomics", + "Cell biology", + "DNA" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "exomedepth", + "Galaxy tool ids": [ + "exomedepth" + ], + "Description": "ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data", + "bio.tool id": "exomedepth", + "bio.tool ids": [ + "exomedepth" + ], + "biii": null, + "bio.tool name": "ExomeDepth", + "bio.tool description": "Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.", + "EDAM operation": [ + "Sequence analysis", + "Variant calling", + "Genotyping", + "Copy number estimation" + ], + "EDAM topic": [ + "Exome sequencing", + "Gene transcripts", + "Mapping", + "Sequencing", + "Genetic variation", + "Rare diseases" + ], + "Status": "To update", + "Source": "https://cran.r-project.org/package=ExomeDepth", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": "exomedepth", + "Galaxy wrapper owner": "crs4", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth", + "Galaxy wrapper version": "1.1.0", + "Conda id": "r-exomedepth", + "Conda version": "1.1.16", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Variant calling", + "Genotyping", + "Copy number estimation" + ], + "EDAM topic (no superclasses)": [ + "Exome sequencing", + "Gene transcripts", + "Mapping", + "Genetic variation", + "Rare diseases" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "exonerate", + "Galaxy tool ids": [ + "exonerate" + ], + "Description": "Exonerate is a generic tool for pairwise sequence comparison.", + "bio.tool id": "exonerate", + "bio.tool ids": [ + "exonerate" + ], + "biii": null, + "bio.tool name": "Exonerate", + "bio.tool description": "A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.", + "EDAM operation": [ + "Pairwise sequence alignment", + "Protein threading", + "Genome alignment" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequence sites, features and motifs", + "Molecular interactions, pathways and networks" + ], + "Status": "Up-to-date", + "Source": "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "exonerate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate", + "Galaxy wrapper version": "2.4.0", + "Conda id": "exonerate", + "Conda version": "2.4.0", + "EDAM operation (no superclasses)": [ + "Pairwise sequence alignment", + "Protein threading", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Sequence sites, features and motifs", + "Molecular interactions, pathways and networks" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "export2graphlan", + "Galaxy tool ids": [ + "export2graphlan" + ], + "Description": "export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn", + "bio.tool id": "export2graphlan", + "bio.tool ids": [ + "export2graphlan" + ], + "biii": null, + "bio.tool name": "export2graphlan", + "bio.tool description": "export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.", + "EDAM operation": [ + "Conversion" + ], + "EDAM topic": [ + "Taxonomy", + "Metabolomics", + "Biomarkers" + ], + "Status": "To update", + "Source": "https://bitbucket.org/CibioCM/export2graphlan/overview", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "export2graphlan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan", + "Galaxy wrapper version": "0.20", + "Conda id": "export2graphlan", + "Conda version": "0.22", + "EDAM operation (no superclasses)": [ + "Conversion" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy", + "Metabolomics", + "Biomarkers" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "extract_genomic_dna", + "Galaxy tool ids": [ + "Extract genomic DNA 1" + ], + "Description": "Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "extract_genomic_dna", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna", + "Galaxy wrapper version": "3.0.3+galaxy2", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "falco", + "Galaxy tool ids": [ + "falco" + ], + "Description": "A high throughput sequence QC analysis tool", + "bio.tool id": "falco", + "bio.tool ids": [ + "falco" + ], + "biii": null, + "bio.tool name": "Falco", + "bio.tool description": "A high-speed FastQC emulation for quality control of sequencing data.", + "EDAM operation": [ + "Sequencing quality control", + "Visualisation", + "Read mapping" + ], + "EDAM topic": [ + "Workflows", + "Mapping", + "Imaging" + ], + "Status": "To update", + "Source": "https://github.com/smithlabcode/falco/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "falco", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco", + "Galaxy wrapper version": "1.2.2+galaxy0", + "Conda id": "falco", + "Conda version": "1.2.2", + "EDAM operation (no superclasses)": [ + "Sequencing quality control", + "Visualisation", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Workflows", + "Mapping", + "Imaging" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fargene", + "Galaxy tool ids": [ + "fargene" + ], + "Description": "fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )", + "bio.tool id": "fargene", + "bio.tool ids": [ + "fargene" + ], + "biii": null, + "bio.tool name": "fARGene", + "bio.tool description": "fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [ + "Metagenomics", + "Microbiology", + "Public health and epidemiology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/fannyhb/fargene", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fargene", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene", + "Galaxy wrapper version": "0.1", + "Conda id": "fargene", + "Conda version": "0.1", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbiology", + "Public health and epidemiology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasta_nucleotide_color_plot", + "Galaxy tool ids": [ + "fasta_nucleotide_color_plot" + ], + "Description": "Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "fasta_nucleotide_color_plot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot", + "Galaxy wrapper version": "1.0.1", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasta_stats", + "Galaxy tool ids": [ + "fasta-stats" + ], + "Description": "Display summary statistics for a fasta file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fasta_stats", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats", + "Galaxy wrapper version": "2.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastani", + "Galaxy tool ids": [ + "fastani" + ], + "Description": "Fast alignment-free computation of whole-genome Average Nucleotide Identity", + "bio.tool id": "fastani", + "bio.tool ids": [ + "fastani" + ], + "biii": null, + "bio.tool name": "FastANI", + "bio.tool description": "FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.", + "EDAM operation": [ + "Genome alignment", + "Sequence similarity search" + ], + "EDAM topic": [ + "Microbiology", + "Genetic variation" + ], + "Status": "To update", + "Source": "https://github.com/ParBLiSS/FastANI", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fastani", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani", + "Galaxy wrapper version": "1.3", + "Conda id": "fastani", + "Conda version": "1.34", + "EDAM operation (no superclasses)": [ + "Genome alignment", + "Sequence similarity search" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastk", + "Galaxy tool ids": [ + "fastk_fastk" + ], + "Description": "FastK: A K-mer counter (for HQ assembly data sets)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/thegenemyers/FASTK", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "fastk", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk", + "Galaxy wrapper version": "1.0.0", + "Conda id": "fastk", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fastp", + "Galaxy tool ids": [ + "fastp" + ], + "Description": "Fast all-in-one preprocessing for FASTQ files", + "bio.tool id": "fastp", + "bio.tool ids": [ + "fastp" + ], + "biii": null, + "bio.tool name": "fastp", + "bio.tool description": "A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.", + "EDAM operation": [ + "Sequencing quality control", + "Sequence contamination filtering" + ], + "EDAM topic": [ + "Sequence analysis", + "Probes and primers" + ], + "Status": "Up-to-date", + "Source": "https://github.com/OpenGene/fastp", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fastp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp", + "Galaxy wrapper version": "0.23.4", + "Conda id": "fastp", + "Conda version": "0.23.4", + "EDAM operation (no superclasses)": [ + "Sequence contamination filtering" + ], + "EDAM topic (no superclasses)": [ + "Probes and primers" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastqc", + "Galaxy tool ids": [ + "fastqc" + ], + "Description": "Read QC reports using FastQC", + "bio.tool id": "fastqc", + "bio.tool ids": [ + "fastqc" + ], + "biii": null, + "bio.tool name": "FastQC", + "bio.tool description": "This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.", + "EDAM operation": [ + "Sequence composition calculation", + "Sequencing quality control", + "Statistical calculation" + ], + "EDAM topic": [ + "Sequencing", + "Data quality management", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastqc", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc", + "Galaxy wrapper version": "0.74+galaxy0", + "Conda id": "fastqc", + "Conda version": "0.12.1", + "EDAM operation (no superclasses)": [ + "Sequence composition calculation", + "Sequencing quality control", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Data quality management", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastqe", + "Galaxy tool ids": [ + "fastqe" + ], + "Description": "FASTQE", + "bio.tool id": "fastqe", + "bio.tool ids": [ + "fastqe" + ], + "biii": null, + "bio.tool name": "FASTQE", + "bio.tool description": "Compute quality stats for FASTQ files and print those stats as emoji... for some reason.", + "EDAM operation": [ + "Sequencing quality control" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequencing" + ], + "Status": "To update", + "Source": "https://fastqe.com/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fastqe", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe", + "Galaxy wrapper version": "0.3.1+galaxy0", + "Conda id": "fastqe", + "Conda version": "0.3.1", + "EDAM operation (no superclasses)": [ + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fasttree", + "Galaxy tool ids": [ + "fasttree" + ], + "Description": "FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL", + "bio.tool id": "fasttree", + "bio.tool ids": [ + "fasttree" + ], + "biii": null, + "bio.tool name": "FastTree", + "bio.tool description": "Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.", + "EDAM operation": [ + "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)" + ], + "EDAM topic": [ + "Phylogenetics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.microbesonline.org/fasttree/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "fasttree", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree", + "Galaxy wrapper version": "2.1.10", + "Conda id": "fasttree", + "Conda version": "2.1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "featurecounts", + "Galaxy tool ids": [ + "featurecounts" + ], + "Description": "featureCounts counts the number of reads aligned to defined masked regions in a reference genome", + "bio.tool id": "featurecounts", + "bio.tool ids": [ + "featurecounts" + ], + "biii": null, + "bio.tool name": "FeatureCounts", + "bio.tool description": "featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.", + "EDAM operation": [ + "Read summarisation", + "RNA-Seq quantification" + ], + "EDAM topic": [ + "RNA-Seq" + ], + "Status": "To update", + "Source": "http://bioinf.wehi.edu.au/featureCounts", + "ToolShed categories": [ + "RNA", + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "featurecounts", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts", + "Galaxy wrapper version": "2.0.3", + "Conda id": "subread", + "Conda version": "2.0.6", + "EDAM operation (no superclasses)": [ + "Read summarisation", + "RNA-Seq quantification" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "feelnc", + "Galaxy tool ids": [ + "feelnc" + ], + "Description": "Galaxy wrapper for FEELnc", + "bio.tool id": "feelnc", + "bio.tool ids": [ + "feelnc" + ], + "biii": null, + "bio.tool name": "FEELnc", + "bio.tool description": "A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.", + "EDAM operation": [ + "Annotation", + "Classification" + ], + "EDAM topic": [ + "RNA-seq", + "Functional, regulatory and non-coding RNA" + ], + "Status": "To update", + "Source": "https://github.com/tderrien/FEELnc", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "feelnc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc", + "Galaxy wrapper version": "0.2.1", + "Conda id": "feelnc", + "Conda version": "0.2", + "EDAM operation (no superclasses)": [ + "Annotation", + "Classification" + ], + "EDAM topic (no superclasses)": [ + "Functional, regulatory and non-coding RNA" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fermikit", + "Galaxy tool ids": [ + "fermi2", + "fermikit_variants" + ], + "Description": "FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/lh3/fermikit", + "ToolShed categories": [ + "Assembly", + "Variant Analysis" + ], + "ToolShed id": "fermikit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit", + "Galaxy wrapper version": "r193", + "Conda id": "fermi2", + "Conda version": "r193", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fgsea", + "Galaxy tool ids": [ + "fgsea" + ], + "Description": "Perform gene set testing using fgsea", + "bio.tool id": "fgsea", + "bio.tool ids": [ + "fgsea" + ], + "biii": null, + "bio.tool name": "fgsea", + "bio.tool description": "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.", + "EDAM operation": [ + "Gene-set enrichment analysis" + ], + "EDAM topic": [ + "Genetics" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/fgsea.html", + "ToolShed categories": [ + "Visualization", + "Transcriptomics", + "Statistics" + ], + "ToolShed id": "fgsea", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea", + "Galaxy wrapper version": "1.8.0+galaxy1", + "Conda id": "bioconductor-fgsea", + "Conda version": "1.28.0", + "EDAM operation (no superclasses)": [ + "Gene-set enrichment analysis" + ], + "EDAM topic (no superclasses)": [ + "Genetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "filtlong", + "Galaxy tool ids": [ + "filtlong" + ], + "Description": "Filtlong - Filtering long reads by quality", + "bio.tool id": "filtlong", + "bio.tool ids": [ + "filtlong" + ], + "biii": null, + "bio.tool name": "Filtlong", + "bio.tool description": "Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.", + "EDAM operation": [ + "Filtering", + "Sequencing quality control" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/rrwick/Filtlong", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "filtlong", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong", + "Galaxy wrapper version": "0.2.1", + "Conda id": "filtlong", + "Conda version": "0.2.1", + "EDAM operation (no superclasses)": [ + "Filtering", + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "flair", + "Galaxy tool ids": [ + "flair_collapse", + "flair_correct" + ], + "Description": "FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/BrooksLabUCSC/flair", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "flair", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair", + "Galaxy wrapper version": "1.5", + "Conda id": "flair", + "Conda version": "2.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "flash", + "Galaxy tool ids": [ + "flash" + ], + "Description": "Fast Length Adjustment of SHort reads", + "bio.tool id": "flash", + "bio.tool ids": [ + "flash" + ], + "biii": null, + "bio.tool name": "FLASH", + "bio.tool description": "Identifies paired-end reads which overlap in the middle, converting them to single long reads", + "EDAM operation": [ + "Read pre-processing", + "Sequence merging", + "Sequence assembly" + ], + "EDAM topic": [ + "Sequencing", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://ccb.jhu.edu/software/FLASH/", + "ToolShed categories": [ + "Assembly", + "Fastq Manipulation" + ], + "ToolShed id": "flash", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash", + "Galaxy wrapper version": "1.2.11", + "Conda id": "flash", + "Conda version": "1.2.11", + "EDAM operation (no superclasses)": [ + "Read pre-processing", + "Sequence merging", + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fraggenescan", + "Galaxy tool ids": [ + "fraggenescan" + ], + "Description": "Tool for finding (fragmented) genes in short read", + "bio.tool id": "fraggenescan", + "bio.tool ids": [ + "fraggenescan" + ], + "biii": null, + "bio.tool name": "FragGeneScan", + "bio.tool description": "Application for finding (fragmented) genes in short reads", + "EDAM operation": [ + "Gene prediction" + ], + "EDAM topic": [ + "Genetics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://sourceforge.net/projects/fraggenescan/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "fraggenescan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan", + "Galaxy wrapper version": null, + "Conda id": "fraggenescan", + "Conda version": "1.31", + "EDAM operation (no superclasses)": [ + "Gene prediction" + ], + "EDAM topic (no superclasses)": [ + "Genetics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "freebayes", + "Galaxy tool ids": [ + "freebayes", + "bamleftalign" + ], + "Description": "Galaxy Freebayes Bayesian genetic variant detector tool", + "bio.tool id": "freebayes", + "bio.tool ids": [ + "freebayes" + ], + "biii": null, + "bio.tool name": "FreeBayes", + "bio.tool description": "Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.", + "EDAM operation": [ + "Variant calling", + "Statistical calculation" + ], + "EDAM topic": [ + "Genomics", + "Genetic variation", + "Rare diseases" + ], + "Status": "To update", + "Source": "https://github.com/ekg/freebayes", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "freebayes", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes", + "Galaxy wrapper version": "1.3.6", + "Conda id": "freebayes", + "Conda version": "1.3.7", + "EDAM operation (no superclasses)": [ + "Variant calling", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Genetic variation", + "Rare diseases" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "freec", + "Galaxy tool ids": [ + "control_freec" + ], + "Description": "Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.", + "bio.tool id": "freec", + "bio.tool ids": [ + "freec" + ], + "biii": null, + "bio.tool name": "FREEC", + "bio.tool description": "A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.", + "EDAM operation": [ + "Copy number estimation", + "Variant calling", + "Genome alignment" + ], + "EDAM topic": [ + "DNA structural variation", + "Oncology", + "Human genetics", + "Data mining" + ], + "Status": "To update", + "Source": "http://boevalab.inf.ethz.ch/FREEC/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "control_freec", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec", + "Galaxy wrapper version": "11.6", + "Conda id": "gawk", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Copy number estimation", + "Variant calling", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Oncology", + "Human genetics", + "Data mining" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "freyja", + "Galaxy tool ids": [ + "freyja_aggregate_plot", + "freyja_boot", + "freyja_demix", + "freyja_variants" + ], + "Description": "lineage abundances estimation", + "bio.tool id": "freyja", + "bio.tool ids": [ + "freyja" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/andersen-lab/Freyja", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": "freyja", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja", + "Galaxy wrapper version": "1.4.4", + "Conda id": "freyja", + "Conda version": "1.5.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fsd", + "Galaxy tool ids": [ + "fsd", + "fsd_beforevsafter", + "fsd_regions", + "td" + ], + "Description": "Tool that plots a histogram of sizes of read families", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics" + ], + "ToolShed id": "duplex_family_size_distribution", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd", + "Galaxy wrapper version": "1.0.2", + "Conda id": "matplotlib", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "funannotate", + "Galaxy tool ids": [ + "funannotate_annotate", + "funannotate_clean", + "funannotate_compare", + "funannotate_predict", + "funannotate_sort" + ], + "Description": "Funannotate is a genome prediction, annotation, and comparison software package.", + "bio.tool id": "funannotate", + "bio.tool ids": [ + "funannotate" + ], + "biii": null, + "bio.tool name": "funannotate", + "bio.tool description": "funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "To update", + "Source": "https://funannotate.readthedocs.io", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate", + "Galaxy wrapper version": "1.8.15", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "gatk4", + "Galaxy tool ids": [ + "gatk4_mutect2" + ], + "Description": "A Galaxy wrapper for Mutect2 from GATK", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://software.broadinstitute.org/gatk/gatk4", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "gatk4_mutect2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4", + "Galaxy wrapper version": "4.1.7.0", + "Conda id": "gatk4", + "Conda version": "4.5.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gdcwebapp", + "Galaxy tool ids": [ + "data_source_gdcwebapp" + ], + "Description": "GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://bioinf.iasi.cnr.it/gdcwebapp/", + "ToolShed categories": [ + "Data Source", + "Convert Formats" + ], + "ToolShed id": "gdcwebapp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/fabio-cumbo/GDCWebApp4Galaxy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp", + "Galaxy wrapper version": "1.0.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gecko", + "Galaxy tool ids": [ + "gecko" + ], + "Description": "Ungapped genome comparison", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/otorreno/gecko", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gecko", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko", + "Galaxy wrapper version": "1.2", + "Conda id": "gecko", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gemini", + "Galaxy tool ids": [ + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_db_info", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_inheritance", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@", + "gemini_@BINARY@" + ], + "Description": "GEMINI: a flexible framework for exploring genome variation", + "bio.tool id": "gemini", + "bio.tool ids": [ + "gemini" + ], + "biii": null, + "bio.tool name": "GEMINI", + "bio.tool description": "GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.", + "EDAM operation": [ + "Sequence analysis", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/arq5x/gemini", + "ToolShed categories": [ + "Sequence Analysis", + "Next Gen Mappers" + ], + "ToolShed id": "gemini", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini", + "Galaxy wrapper version": "0.20.1", + "Conda id": "gemini", + "Conda version": "0.30.2", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "genebed_maf_to_fasta", + "Galaxy tool ids": [ + "GeneBed_Maf_Fasta2" + ], + "Description": "Stitch gene blocks given a set of coding exon intervals", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "genebed_maf_to_fasta", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta", + "Galaxy wrapper version": "1.0.1+galaxy0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "genehunter_modscore", + "Galaxy tool ids": [ + "genehunter_modscore" + ], + "Description": "Maximised LOD score pedigree analysis utility", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "genehunter_modscore", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore", + "Galaxy wrapper version": "3.0.0", + "Conda id": "ghm", + "Conda version": "3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "geneiobio", + "Galaxy tool ids": [ + "gene_iobio_display_generation_iframe" + ], + "Description": "Gene.iobio is an interactive tool for variant and trio analysis.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/iobio/gene.iobio", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "geneiobio", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio", + "Galaxy wrapper version": "4.7.1+galaxy1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "genetrack", + "Galaxy tool ids": [ + "genetrack" + ], + "Description": "Contains a tool that separately identifies peaks on the forward \"+” (W) and reverse “-” (C) strand.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "genetrack", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack", + "Galaxy wrapper version": null, + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "genomescope", + "Galaxy tool ids": [ + "genomescope" + ], + "Description": "Analyze unassembled short reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/tbenavi1/genomescope2.0", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "genomescope", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope", + "Galaxy wrapper version": "2.0", + "Conda id": "genomescope2", + "Conda version": "2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "genomic_super_signature", + "Galaxy tool ids": [ + "genomic_super_signature" + ], + "Description": "Interpretation of RNAseq experiments through robust, efficient comparison to public databases", + "bio.tool id": "genomicsupersignature", + "bio.tool ids": [ + "genomicsupersignature" + ], + "biii": null, + "bio.tool name": "GenomicSuperSignature", + "bio.tool description": "GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.", + "EDAM operation": [ + "Gene-set enrichment analysis", + "Essential dynamics", + "Deposition", + "Principal component visualisation", + "Dimensionality reduction" + ], + "EDAM topic": [ + "RNA-Seq", + "Transcriptomics", + "Microbial ecology", + "Genotype and phenotype", + "Microarray experiment" + ], + "Status": "To update", + "Source": "https://github.com/shbrief/GenomicSuperSignature", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "Transcriptomics" + ], + "ToolShed id": "genomic_super_signature", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature", + "Galaxy wrapper version": "1.2.0", + "Conda id": "bioconductor-genomicsupersignature", + "Conda version": "1.10.0", + "EDAM operation (no superclasses)": [ + "Gene-set enrichment analysis", + "Essential dynamics", + "Deposition", + "Principal component visualisation", + "Dimensionality reduction" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Transcriptomics", + "Microbial ecology", + "Genotype and phenotype", + "Microarray experiment" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "genrich", + "Galaxy tool ids": [ + "genrich" + ], + "Description": "Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/jsh58/Genrich", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "genrich", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/jsh58/Genrich", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich", + "Galaxy wrapper version": "0.5+galaxy2", + "Conda id": "genrich", + "Conda version": "0.6.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "get_hrun", + "Galaxy tool ids": [ + "get_hrun" + ], + "Description": "Annotate indel variants with homopolymer context", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "get_hrun", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun", + "Galaxy wrapper version": "0.5.9.2", + "Conda id": "pyfaidx", + "Conda version": "0.8.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "getorganelle", + "Galaxy tool ids": [ + "get_annotated_regions_from_gb", + "get_organelle_from_reads" + ], + "Description": "GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.", + "bio.tool id": "getorganelle", + "bio.tool ids": [ + "getorganelle" + ], + "biii": null, + "bio.tool name": "GetOrganelle", + "bio.tool description": "A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.", + "EDAM operation": [ + "De-novo assembly", + "Genome assembly", + "Mapping assembly", + "Mapping", + "Sequence trimming" + ], + "EDAM topic": [ + "Cell biology", + "Sequence assembly", + "Whole genome sequencing", + "Plant biology", + "Model organisms" + ], + "Status": "Up-to-date", + "Source": "https://github.com/Kinggerm/GetOrganelle", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "getorganelle", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle", + "Galaxy wrapper version": "1.7.7.1", + "Conda id": "getorganelle", + "Conda version": "1.7.7.1", + "EDAM operation (no superclasses)": [ + "De-novo assembly", + "Genome assembly", + "Mapping assembly", + "Mapping", + "Sequence trimming" + ], + "EDAM topic (no superclasses)": [ + "Cell biology", + "Sequence assembly", + "Whole genome sequencing", + "Plant biology", + "Model organisms" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gfa_to_fa", + "Galaxy tool ids": [ + "gfa_to_fa" + ], + "Description": "gfa_to_fa - Converting GFA format to Fasta format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://gfa-spec.github.io/GFA-spec/", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "gfa_to_fa", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa", + "Galaxy wrapper version": "0.1.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "gff3_rebase", + "Galaxy tool ids": [ + "gff3.rebase" + ], + "Description": "Rebase a GFF against a parent GFF (e.g. an original genome)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gff3_rebase", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase", + "Galaxy wrapper version": "1.2", + "Conda id": "bcbiogff", + "Conda version": "0.6.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "gffcompare", + "Galaxy tool ids": [ + "gffcompare" + ], + "Description": "Galaxy wrappers for Geo Pertea's GffCompare package.", + "bio.tool id": "gffcompare", + "bio.tool ids": [ + "gffcompare" + ], + "biii": null, + "bio.tool name": "gffcompare", + "bio.tool description": "Program for comparing, annotating, merging and tracking transcripts in GFF files.", + "EDAM operation": [ + "Sequence annotation" + ], + "EDAM topic": [ + "Nucleic acids", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/gpertea/gffcompare/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gffcompare", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare", + "Galaxy wrapper version": "0.12.6", + "Conda id": "gffcompare", + "Conda version": "0.12.6", + "EDAM operation (no superclasses)": [ + "Sequence annotation" + ], + "EDAM topic (no superclasses)": [ + "Nucleic acids", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "gffread", + "Galaxy tool ids": [ + "gffread" + ], + "Description": "gffread filters and/or converts GFF3/GTF2 records", + "bio.tool id": "gffread", + "bio.tool ids": [ + "gffread" + ], + "biii": null, + "bio.tool name": "gffread", + "bio.tool description": "program for filtering, converting and manipulating GFF files", + "EDAM operation": [ + "Sequence annotation" + ], + "EDAM topic": [ + "Nucleic acids", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gffread", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread", + "Galaxy wrapper version": "0.12.7", + "Conda id": "gffread", + "Conda version": "0.12.7", + "EDAM operation (no superclasses)": [ + "Sequence annotation" + ], + "EDAM topic (no superclasses)": [ + "Nucleic acids", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ggplot2", + "Galaxy tool ids": [ + "ggplot2_heatmap", + "ggplot2_pca", + "ggplot2_histogram", + "ggplot2_point", + "ggplot2_violin" + ], + "Description": "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.", + "bio.tool id": "ggplot2", + "bio.tool ids": [ + "ggplot2" + ], + "biii": null, + "bio.tool name": "ggplot2", + "bio.tool description": "Plotting system for R, based on the grammar of graphics.", + "EDAM operation": [ + "Visualisation" + ], + "EDAM topic": [ + "Data visualisation" + ], + "Status": "To update", + "Source": "https://github.com/tidyverse/ggplot2", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2", + "Galaxy wrapper version": "3.4.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Data visualisation" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "ggupset", + "Galaxy tool ids": [ + "emc-ggupset" + ], + "Description": "Create Upset Plots with ggupset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/const-ae/ggupset", + "ToolShed categories": [ + "Graphics" + ], + "ToolShed id": "ggupset", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset", + "Galaxy wrapper version": "1.0", + "Conda id": "r-ggupset", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "glimmer", + "Galaxy tool ids": [ + "glimmer_acgt_content", + "glimmer_build_icm", + "glimmer_extract", + "glimmer_gbk_to_orf", + "glimmer_glimmer_to_gff", + "glimmer_long_orfs", + "glimmer_knowledge_based", + "glimmer_not_knowledge_based" + ], + "Description": "Glimmer makes gene predictions.", + "bio.tool id": "gemini", + "bio.tool ids": [ + "gemini" + ], + "biii": null, + "bio.tool name": "GEMINI", + "bio.tool description": "GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.", + "EDAM operation": [ + "Sequence analysis", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://ccb.jhu.edu/software/glimmer/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer", + "Galaxy wrapper version": null, + "Conda id": "glimmer", + "Conda version": "3.02", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "goenrichment", + "Galaxy tool ids": [ + "goenrichment", + "goslimmer" + ], + "Description": "Performs GO Enrichment analysis.", + "bio.tool id": "goenrichment", + "bio.tool ids": [ + "goenrichment" + ], + "biii": null, + "bio.tool name": "GOEnrichment", + "bio.tool description": "GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.", + "EDAM operation": [ + "Gene-set enrichment analysis" + ], + "EDAM topic": [ + "Transcriptomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/DanFaria/GOEnrichment", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment", + "Galaxy wrapper version": "2.0.1", + "Conda id": "goenrichment", + "Conda version": "2.0.1", + "EDAM operation (no superclasses)": [ + "Gene-set enrichment analysis" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "goseq", + "Galaxy tool ids": [ + "goseq" + ], + "Description": "goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data", + "bio.tool id": "goseq", + "bio.tool ids": [ + "goseq" + ], + "biii": null, + "bio.tool name": "GOseq", + "bio.tool description": "Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.", + "EDAM operation": [ + "Gene functional annotation" + ], + "EDAM topic": [ + "RNA-Seq" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/goseq.html", + "ToolShed categories": [ + "Statistics", + "RNA", + "Micro-array Analysis" + ], + "ToolShed id": "goseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq", + "Galaxy wrapper version": "1.50.0", + "Conda id": "bioconductor-goseq", + "Conda version": "1.54.0", + "EDAM operation (no superclasses)": [ + "Gene functional annotation" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "gprofiler", + "Galaxy tool ids": [ + "gprofiler_convert", + "gprofiler_gost", + "gprofiler_orth", + "gprofiler_random", + "gprofiler_snpense" + ], + "Description": "functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://biit.cs.ut.ee/gprofiler", + "ToolShed categories": [ + "Statistics", + "Web Services" + ], + "ToolShed id": "gprofiler", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler", + "Galaxy wrapper version": "@TOOL_VERSION@+galaxy11", + "Conda id": "r-gprofiler2", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "graphembed", + "Galaxy tool ids": [ + "graphembed" + ], + "Description": "Compute a 2D embedding of a data matrix given supervised class information", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/fabriziocosta/GraphEmbed", + "ToolShed categories": [ + "Statistics", + "Graphics" + ], + "ToolShed id": "graphembed", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed", + "Galaxy wrapper version": "2.4", + "Conda id": "graph_embed", + "Conda version": "2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "graphlan", + "Galaxy tool ids": [ + "graphlan", + "graphlan_annotate" + ], + "Description": "GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees", + "bio.tool id": "graphlan", + "bio.tool ids": [ + "graphlan" + ], + "biii": null, + "bio.tool name": "GraPhlAn", + "bio.tool description": "GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.", + "EDAM operation": [ + "Phylogenetic inference", + "Phylogenetic tree visualisation", + "Phylogenetic tree editing", + "Taxonomic classification" + ], + "EDAM topic": [ + "Metagenomics", + "Phylogenetics", + "Phylogenomics", + "Cladistics" + ], + "Status": "To update", + "Source": "https://github.com/biobakery/graphlan", + "ToolShed categories": [ + "Metagenomics", + "Graphics", + "Phylogenetics" + ], + "ToolShed id": "graphlan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan", + "Galaxy wrapper version": null, + "Conda id": "graphlan", + "Conda version": "1.1.3", + "EDAM operation (no superclasses)": [ + "Phylogenetic inference", + "Phylogenetic tree visualisation", + "Phylogenetic tree editing", + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Phylogenetics", + "Phylogenomics", + "Cladistics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "gtdbtk", + "Galaxy tool ids": [ + "gtdbtk_classify_wf" + ], + "Description": "GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. ", + "bio.tool id": "GTDB-Tk", + "bio.tool ids": [ + "GTDB-Tk" + ], + "biii": null, + "bio.tool name": "GTDB-Tk", + "bio.tool description": "a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).", + "EDAM operation": [ + "Genome alignment", + "Taxonomic classification", + "Sequence assembly", + "Query and retrieval" + ], + "EDAM topic": [ + "Metagenomics", + "Taxonomy", + "Phylogenetics", + "Database management", + "Proteins" + ], + "Status": "To update", + "Source": "https://github.com/Ecogenomics/GTDBTk", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "gtdbtk", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk", + "Galaxy wrapper version": "2.3.2", + "Conda id": "gtdbtk", + "Conda version": "2.4.0", + "EDAM operation (no superclasses)": [ + "Genome alignment", + "Taxonomic classification", + "Sequence assembly", + "Query and retrieval" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Taxonomy", + "Phylogenetics", + "Database management", + "Proteins" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gtfToBed12", + "Galaxy tool ids": [ + "gtftobed12" + ], + "Description": "Convert GTF files to BED12 format", + "bio.tool id": "UCSC_Genome_Browser_Utilities", + "bio.tool ids": [ + "UCSC_Genome_Browser_Utilities" + ], + "biii": null, + "bio.tool name": "UCSC Genome Browser Utilities", + "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "gtftobed12", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12", + "Galaxy wrapper version": "357", + "Conda id": "ucsc-gtftogenepred", + "Conda version": "447", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "gubbins", + "Galaxy tool ids": [ + "gubbins" + ], + "Description": "Gubbins - bacterial recombination detection", + "bio.tool id": "gubbins", + "bio.tool ids": [ + "gubbins" + ], + "biii": null, + "bio.tool name": "Gubbins", + "bio.tool description": "Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.", + "EDAM operation": [ + "Genotyping", + "Phylogenetic inference", + "Ancestral reconstruction" + ], + "EDAM topic": [ + "Phylogeny", + "Genotype and phenotype", + "Whole genome sequencing" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gubbins", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins", + "Galaxy wrapper version": "3.2.1", + "Conda id": "gubbins", + "Conda version": "3.3.5", + "EDAM operation (no superclasses)": [ + "Genotyping", + "Phylogenetic inference", + "Ancestral reconstruction" + ], + "EDAM topic (no superclasses)": [ + "Phylogeny", + "Genotype and phenotype", + "Whole genome sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gvcftools", + "Galaxy tool ids": [ + "gvcftools_extract_variants" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/sequencing/gvcftools", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools", + "Galaxy wrapper version": "0.1", + "Conda id": "gvcftools", + "Conda version": "0.17.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gwastools", + "Galaxy tool ids": [ + "gwastools_manhattan_plot" + ], + "Description": null, + "bio.tool id": "gwastools", + "bio.tool ids": [ + "gwastools" + ], + "biii": null, + "bio.tool name": "GWASTools", + "bio.tool description": "Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.", + "EDAM operation": [ + "Deposition", + "Analysis", + "Annotation" + ], + "EDAM topic": [ + "GWAS study" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/GWASTools.html", + "ToolShed categories": [ + "Visualization", + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools", + "Galaxy wrapper version": "0.1.0", + "Conda id": "bioconductor-gwastools", + "Conda version": "1.48.0", + "EDAM operation (no superclasses)": [ + "Deposition", + "Analysis", + "Annotation" + ], + "EDAM topic (no superclasses)": [ + "GWAS study" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hamronization", + "Galaxy tool ids": [ + "hamronize_summarize", + "hamronize_tool" + ], + "Description": "Convert AMR gene detection tool output to hAMRonization specification format.", + "bio.tool id": "hamronization", + "bio.tool ids": [ + "hamronization" + ], + "biii": null, + "bio.tool name": "hAMRonization", + "bio.tool description": "Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure", + "EDAM operation": [ + "Data handling", + "Antimicrobial resistance prediction", + "Parsing" + ], + "EDAM topic": [ + "Public health and epidemiology", + "Microbiology", + "Bioinformatics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pha4ge/hAMRonization", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "hamronization", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization", + "Galaxy wrapper version": "1.1.4", + "Conda id": "hamronization", + "Conda version": "1.1.4", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction", + "Parsing" + ], + "EDAM topic (no superclasses)": [ + "Public health and epidemiology", + "Microbiology", + "Bioinformatics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "hansel", + "Galaxy tool ids": [ + "bio_hansel" + ], + "Description": "Heidelberg and Enteritidis SNP Elucidation", + "bio.tool id": "Biohansel", + "bio.tool ids": [ + "Biohansel" + ], + "biii": null, + "bio.tool name": "BioHansel", + "bio.tool description": "BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.", + "EDAM operation": [ + "Genotyping", + "SNP detection", + "Genome assembly" + ], + "EDAM topic": [ + "Whole genome sequencing", + "DNA polymorphism", + "Genotype and phenotype", + "Infectious disease", + "Agricultural science" + ], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/bio_hansel", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "bio_hansel", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel", + "Galaxy wrapper version": "2.6.1", + "Conda id": "bio_hansel", + "Conda version": "2.6.1", + "EDAM operation (no superclasses)": [ + "Genotyping", + "SNP detection", + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "DNA polymorphism", + "Genotype and phenotype", + "Infectious disease", + "Agricultural science" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hapcut2", + "Galaxy tool ids": [ + "hapcut2" + ], + "Description": "Robust and accurate haplotype assembly for diverse sequencing technologies", + "bio.tool id": "hapcut2", + "bio.tool ids": [ + "hapcut2" + ], + "biii": null, + "bio.tool name": "HapCUT2", + "bio.tool description": "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to \"just work\" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md", + "EDAM operation": [ + "Haplotype mapping", + "Variant classification" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/vibansal/HapCUT2", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hapcut2", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2", + "Galaxy wrapper version": "1.3.4", + "Conda id": "hapcut2", + "Conda version": "1.3.4", + "EDAM operation (no superclasses)": [ + "Haplotype mapping", + "Variant classification" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hapog", + "Galaxy tool ids": [ + "hapog" + ], + "Description": "Hapo-G - Haplotype-Aware Polishing of Genomes", + "bio.tool id": "hapog", + "bio.tool ids": [ + "hapog" + ], + "biii": null, + "bio.tool name": "Hapo-G", + "bio.tool description": "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.", + "EDAM operation": [ + "Genome assembly", + "Optimisation and refinement" + ], + "EDAM topic": [ + "Sequence assembly", + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/institut-de-genomique/HAPO-G", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hapog", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog", + "Galaxy wrapper version": "1.3.8", + "Conda id": "hapog", + "Conda version": "1.3.8", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Optimisation and refinement" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "happy", + "Galaxy tool ids": [ + "som.py" + ], + "Description": "A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.", + "bio.tool id": "hap.py", + "bio.tool ids": [ + "hap.py" + ], + "biii": null, + "bio.tool name": "hap.py", + "bio.tool description": "This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.", + "EDAM operation": [ + "Variant calling", + "Sequence analysis", + "Genotyping" + ], + "EDAM topic": [ + "Genomics", + "DNA polymorphism" + ], + "Status": "To update", + "Source": "https://github.com/Illumina/hap.py", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "happy", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy", + "Galaxy wrapper version": "0.3.14", + "Conda id": "hap.py", + "Conda version": "0.3.15", + "EDAM operation (no superclasses)": [ + "Variant calling", + "Sequence analysis", + "Genotyping" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "DNA polymorphism" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "heatmap2", + "Galaxy tool ids": [ + "ggplot2_heatmap2" + ], + "Description": "heatmap.2 function from the R gplots package", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/cran/gplots", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "ggplot2_heatmap2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2", + "Galaxy wrapper version": "3.1.3.1", + "Conda id": "r-gplots", + "Conda version": "2.17.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "heinz", + "Galaxy tool ids": [ + "heinz_bum", + "heinz", + "heinz_scoring", + "heinz_visualization" + ], + "Description": "An algorithm for identification of the optimal scoring subnetwork.", + "bio.tool id": "heinz", + "bio.tool ids": [ + "heinz", + "bionet" + ], + "biii": null, + "bio.tool name": "Heinz", + "bio.tool description": "Tool for single-species active module discovery.", + "EDAM operation": [ + "Pathway or network analysis" + ], + "EDAM topic": [ + "Genetics", + "Gene expression", + "Molecular interactions, pathways and networks" + ], + "Status": "To update", + "Source": "https://github.com/ls-cwi/heinz", + "ToolShed categories": [ + "Transcriptomics", + "Visualization", + "Statistics" + ], + "ToolShed id": "heinz", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz", + "Galaxy wrapper version": "1.0", + "Conda id": "bioconductor-bionet", + "Conda version": "1.62.0", + "EDAM operation (no superclasses)": [ + "Pathway or network analysis" + ], + "EDAM topic (no superclasses)": [ + "Genetics", + "Gene expression", + "Molecular interactions, pathways and networks" + ], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hicexplorer", + "Galaxy tool ids": [ + "hicexplorer_chicaggregatestatistic", + "hicexplorer_chicdifferentialtest", + "hicexplorer_chicexportdata", + "hicexplorer_chicplotviewpoint", + "hicexplorer_chicqualitycontrol", + "hicexplorer_chicsignificantinteractions", + "hicexplorer_chicviewpoint", + "hicexplorer_chicviewpointbackgroundmodel", + "hicexplorer_hicadjustmatrix", + "hicexplorer_hicaggregatecontacts", + "hicexplorer_hicaverageregions", + "hicexplorer_hicbuildmatrix", + "hicexplorer_hiccomparematrices", + "hicexplorer_hiccompartmentspolarization", + "hicexplorer_hicconvertformat", + "hicexplorer_hiccorrectmatrix", + "hicexplorer_hiccorrelate", + "hicexplorer_hicdetectloops", + "hicexplorer_hicdifferentialtad", + "hicexplorer_hicfindrestrictionsites", + "hicexplorer_hicfindtads", + "hicexplorer_hichyperoptDetectLoops", + "hicexplorer_hicinfo", + "hicexplorer_hicinterintratad", + "hicexplorer_hicmergedomains", + "hicexplorer_hicmergeloops", + "hicexplorer_hicmergematrixbins", + "hicexplorer_hicnormalize", + "hicexplorer_hicpca", + "hicexplorer_hicplotaverageregions", + "hicexplorer_hicplotdistvscounts", + "hicexplorer_hicplotmatrix", + "hicexplorer_hicplotsvl", + "hicexplorer_hicplotviewpoint", + "hicexplorer_hicquickqc", + "hicexplorer_hicsummatrices", + "hicexplorer_hictadclassifier", + "hicexplorer_hictraintadclassifier", + "hicexplorer_hictransform", + "hicexplorer_hicvalidatelocations" + ], + "Description": "HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/deeptools/HiCExplorer", + "ToolShed categories": [ + "Sequence Analysis", + "Visualization" + ], + "ToolShed id": "hicexplorer", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer", + "Galaxy wrapper version": "3.7.2", + "Conda id": "hicexplorer", + "Conda version": "3.7.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 40, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "hicstuff", + "Galaxy tool ids": [ + "hicstuff_pipeline" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/koszullab/hicstuff", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff", + "Galaxy wrapper version": "3.1.5", + "Conda id": "hicstuff", + "Conda version": "3.2.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hifiasm_meta", + "Galaxy tool ids": [ + "hifiasm_meta" + ], + "Description": "A hifiasm fork for metagenome assembly using Hifi reads.", + "bio.tool id": "hifiasm-meta", + "bio.tool ids": [ + "hifiasm-meta" + ], + "biii": null, + "bio.tool name": "Hifiasm-meta", + "bio.tool description": "Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.", + "EDAM operation": [ + "Sequence assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Metagenomics" + ], + "Status": "To update", + "Source": "https://github.com/xfengnefx/hifiasm-meta", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "hifiasm_meta", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta", + "Galaxy wrapper version": "0.3.1", + "Conda id": "hifiasm_meta", + "Conda version": "hamtv0.3.1", + "EDAM operation (no superclasses)": [ + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hisat2", + "Galaxy tool ids": [ + "hisat2" + ], + "Description": "HISAT2 is a fast and sensitive spliced alignment program.", + "bio.tool id": "hisat2", + "bio.tool ids": [ + "hisat2" + ], + "biii": null, + "bio.tool name": "HISAT2", + "bio.tool description": "Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "RNA-seq" + ], + "Status": "Up-to-date", + "Source": "http://ccb.jhu.edu/software/hisat2/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hisat2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2", + "Galaxy wrapper version": "2.2.1", + "Conda id": "hisat2", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "hivclustering", + "Galaxy tool ids": [ + "hivclustering" + ], + "Description": "Infers transmission networks from pairwise distances inferred by tn93", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pypi.org/project/hivclustering/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "hivclustering", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering", + "Galaxy wrapper version": "1.3.1", + "Conda id": "python-hivclustering", + "Conda version": "1.6.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hmmer3", + "Galaxy tool ids": [ + "hmmer_alimask", + "hmmer_hmmalign", + "hmmer_hmmbuild", + "hmmer_hmmconvert", + "hmmer_hmmemit", + "hmmer_hmmfetch", + "hmmer_hmmscan", + "hmmer_hmmsearch", + "hmmer_jackhmmer", + "hmmer_nhmmer", + "hmmer_nhmmscan", + "hmmer_phmmer" + ], + "Description": "HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).", + "bio.tool id": "hmmer3", + "bio.tool ids": [ + "hmmer3" + ], + "biii": null, + "bio.tool name": "HMMER3", + "bio.tool description": "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.", + "EDAM operation": [ + "Formatting", + "Multiple sequence alignment", + "Sequence profile generation", + "Format validation", + "Conversion", + "Sequence generation", + "Data retrieval", + "Statistical calculation", + "Database search", + "Formatting", + "Database search", + "Database search", + "Probabilistic sequence generation", + "Statistical calculation", + "Statistical calculation", + "Sequence database search", + "Formatting", + "Sequence database search", + "Database search", + "Sequence database search" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequence sites, features and motifs", + "Gene and protein families" + ], + "Status": "Up-to-date", + "Source": "http://hmmer.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3", + "Galaxy wrapper version": "3.4", + "Conda id": "hmmer", + "Conda version": "3.4", + "EDAM operation (no superclasses)": [ + "Formatting", + "Multiple sequence alignment", + "Sequence profile generation", + "Format validation", + "Conversion", + "Data retrieval", + "Statistical calculation", + "Formatting", + "Probabilistic sequence generation", + "Statistical calculation", + "Statistical calculation", + "Sequence database search", + "Formatting", + "Sequence database search", + "Sequence database search" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Sequence sites, features and motifs", + "Gene and protein families" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 12, + "Available on UseGalaxy.org.fr": 12 + }, + { + "Galaxy wrapper id": "homer", + "Galaxy tool ids": [ + "homer_annotatePeaks", + "homer_findMotifs", + "homer_findMotifsGenome", + "homer_gtf_to_annotations", + "homer_scanMotifGenomeWide" + ], + "Description": "HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.", + "bio.tool id": "homer", + "bio.tool ids": [ + "homer" + ], + "biii": null, + "bio.tool name": "homer", + "bio.tool description": "HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.", + "EDAM operation": [ + "Sequence motif discovery" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://homer.ucsd.edu/homer/index.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "data_manager_homer_preparse", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer", + "Galaxy wrapper version": "4.11", + "Conda id": "homer", + "Conda version": "4.11", + "EDAM operation (no superclasses)": [ + "Sequence motif discovery" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "htseq_count", + "Galaxy tool ids": [ + "htseq_count" + ], + "Description": "Count aligned reads (SAM/BAM) that overlap genomic features (GFF)", + "bio.tool id": "htseq", + "bio.tool ids": [ + "htseq" + ], + "biii": null, + "bio.tool name": "HTSeq", + "bio.tool description": "Python framework to process and analyse high-throughput sequencing (HTS) data", + "EDAM operation": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://readthedocs.org/projects/htseq/", + "ToolShed categories": [ + "Genomic Interval Operations", + "SAM", + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "htseq_count", + "Galaxy wrapper owner": "lparsons", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count", + "Galaxy wrapper version": "2.0.5", + "Conda id": "htseq", + "Conda version": "2.0.5", + "EDAM operation (no superclasses)": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "humann", + "Galaxy tool ids": [ + "humann", + "humann_associate", + "humann_barplot", + "humann_join_tables", + "humann_reduce_table", + "humann_regroup_table", + "humann_rename_table", + "humann_renorm_table", + "humann_rna_dna_norm", + "humann_split_stratified_table", + "humann_split_table", + "humann_strain_profiler", + "humann_unpack_pathways" + ], + "Description": "HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution", + "bio.tool id": "humann", + "bio.tool ids": [ + "humann" + ], + "biii": null, + "bio.tool name": "humann", + "bio.tool description": "HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”", + "EDAM operation": [ + "Species frequency estimation", + "Taxonomic classification", + "Phylogenetic analysis" + ], + "EDAM topic": [ + "Metagenomics", + "Phylogenomics" + ], + "Status": "Up-to-date", + "Source": "http://huttenhower.sph.harvard.edu/humann", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "humann", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann", + "Galaxy wrapper version": "3.8", + "Conda id": "humann", + "Conda version": "3.8", + "EDAM operation (no superclasses)": [ + "Species frequency estimation", + "Taxonomic classification", + "Phylogenetic analysis" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Phylogenomics" + ], + "Available on UseGalaxy.org": 6, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 13, + "Available on UseGalaxy.org.fr": 13 + }, + { + "Galaxy wrapper id": "hybpiper", + "Galaxy tool ids": [ + "hybpiper" + ], + "Description": "Analyse targeted sequence capture data", + "bio.tool id": "HybPiper", + "bio.tool ids": [ + "HybPiper" + ], + "biii": null, + "bio.tool name": "HybPiper", + "bio.tool description": "Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.", + "EDAM operation": [ + "Sequence trimming", + "Sequence assembly", + "Read mapping" + ], + "EDAM topic": [ + "Phylogenetics", + "Plant biology", + "Gene transcripts", + "Sequence assembly", + "Phylogenomics" + ], + "Status": "To update", + "Source": "https://github.com/mossmatters/HybPiper", + "ToolShed categories": [ + "Sequence Analysis", + "Phylogenetics" + ], + "ToolShed id": "hybpiper", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper", + "Galaxy wrapper version": "2.1.6", + "Conda id": "hybpiper", + "Conda version": "2.1.7", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "Sequence assembly", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics", + "Plant biology", + "Gene transcripts", + "Sequence assembly", + "Phylogenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hyphy", + "Galaxy tool ids": [ + "hyphy_absrel", + "hyphy_annotate", + "hyphy_bgm", + "hyphy_busted", + "hyphy_cfel", + "hyphy_conv", + "hyphy_fade", + "hyphy_fel", + "hyphy_fubar", + "hyphy_gard", + "hyphy_meme", + "hyphy_prime", + "hyphy_relax", + "hyphy_slac", + "hyphy_sm19", + "hyphy_strike_ambigs", + "hyphy_summary" + ], + "Description": "Hypothesis Testing using Phylogenies", + "bio.tool id": "HyPhy", + "bio.tool ids": [ + "HyPhy" + ], + "biii": null, + "bio.tool name": "HyPhy", + "bio.tool description": "Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.", + "EDAM operation": [ + "Statistical calculation" + ], + "EDAM topic": [ + "Phylogeny", + "Small molecules", + "Molecular interactions, pathways and networks" + ], + "Status": "To update", + "Source": "http://www.hyphy.org", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy", + "Galaxy wrapper version": "2.5.47", + "Conda id": "hyphy", + "Conda version": "2.5.62", + "EDAM operation (no superclasses)": [ + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Phylogeny", + "Small molecules", + "Molecular interactions, pathways and networks" + ], + "Available on UseGalaxy.org": 17, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 17, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "hypo", + "Galaxy tool ids": [ + "hypo" + ], + "Description": "Super Fast & Accurate Polisher for Long Read Genome Assemblies", + "bio.tool id": "HyPo", + "bio.tool ids": [ + "HyPo" + ], + "biii": null, + "bio.tool name": "HyPo", + "bio.tool description": "HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.", + "EDAM operation": [ + "Optimisation and refinement", + "Genome assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/kensung-lab/hypo", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "hypo", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo", + "Galaxy wrapper version": "1.0.3", + "Conda id": "hypo", + "Conda version": "1.0.3", + "EDAM operation (no superclasses)": [ + "Optimisation and refinement", + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "icescreen", + "Galaxy tool ids": [ + "icescreen" + ], + "Description": "ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.", + "bio.tool id": "icescreen", + "bio.tool ids": [ + "icescreen" + ], + "biii": null, + "bio.tool name": "ICEscreen", + "bio.tool description": "A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.", + "EDAM operation": [ + "Database search", + "Protein feature detection" + ], + "EDAM topic": [ + "Mobile genetic elements", + "Sequence sites, features and motifs", + "Genomics", + "Molecular interactions, pathways and networks", + "Structural variation" + ], + "Status": "To update", + "Source": "https://icescreen.migale.inrae.fr/", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "icescreen", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://forgemia.inra.fr/ices_imes_analysis/icescreen", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen", + "Galaxy wrapper version": "1.3.1", + "Conda id": "icescreen", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [ + "Database search", + "Protein feature detection" + ], + "EDAM topic (no superclasses)": [ + "Mobile genetic elements", + "Sequence sites, features and motifs", + "Genomics", + "Molecular interactions, pathways and networks", + "Structural variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "idba_ud", + "Galaxy tool ids": [ + "idba_hybrid", + "idba_tran", + "idba_ud" + ], + "Description": "Wrappers for the idba assembler variants.", + "bio.tool id": "idba", + "bio.tool ids": [ + "idba" + ], + "biii": null, + "bio.tool name": "IDBA", + "bio.tool description": "A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.", + "EDAM operation": [ + "Sequence assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://i.cs.hku.hk/~alse/hkubrg/projects/index.html", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "idba", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud", + "Galaxy wrapper version": null, + "Conda id": "idba", + "Conda version": "1.1.3", + "EDAM operation (no superclasses)": [ + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "idr", + "Galaxy tool ids": [ + "idr" + ], + "Description": "Galaxy wrappers for the IDR package from Nathan Boleu", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nboley/idr", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "idr", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr", + "Galaxy wrapper version": "2.0.3", + "Conda id": "idr", + "Conda version": "2.0.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "idr_download", + "Galaxy tool ids": [ + "idr_download_by_ids" + ], + "Description": "Image Data Resource downloading tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://idr.openmicroscopy.org", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "idr_download_by_ids", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download", + "Galaxy wrapper version": "0.44.1", + "Conda id": "omero-py", + "Conda version": "5.11.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "iedb_api", + "Galaxy tool ids": [ + "iedb_api" + ], + "Description": "Get epitope binding predictions from IEDB-API", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://tools.immuneepitope.org/main/tools-api/", + "ToolShed categories": [ + "Data Source", + "Sequence Analysis" + ], + "ToolShed id": "iedb_api", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api", + "Galaxy wrapper version": "2.15.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "instrain", + "Galaxy tool ids": [ + "instrain_compare", + "instrain_profile" + ], + "Description": "InStrain is a tool for analysis of co-occurring genome populations from metagenomes", + "bio.tool id": "instrain", + "bio.tool ids": [ + "instrain" + ], + "biii": null, + "bio.tool name": "InStrain", + "bio.tool description": "InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification", + "EDAM operation": [ + "SNP detection", + "Genome comparison" + ], + "EDAM topic": [ + "Mapping", + "Metagenomics" + ], + "Status": "To update", + "Source": "https://instrain.readthedocs.io/en/latest/#", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "instrain", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain", + "Galaxy wrapper version": "1.5.3", + "Conda id": "instrain", + "Conda version": "1.9.0", + "EDAM operation (no superclasses)": [ + "SNP detection", + "Genome comparison" + ], + "EDAM topic (no superclasses)": [ + "Mapping", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "integron_finder", + "Galaxy tool ids": [ + "integron_finder" + ], + "Description": "\"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching\"", + "bio.tool id": "integron_finder", + "bio.tool ids": [ + "integron_finder" + ], + "biii": null, + "bio.tool name": "Integron Finder", + "bio.tool description": "A tool to detect Integron in DNA sequences.", + "EDAM operation": [ + "Nucleic acid feature detection", + "Sequence motif recognition", + "Protein feature detection", + "Genome annotation" + ], + "EDAM topic": [ + "Functional genomics", + "Mobile genetic elements", + "Molecular biology", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/gem-pasteur/Integron_Finder", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "integronfinder", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder", + "Galaxy wrapper version": "2.0.3", + "Conda id": "integron_finder", + "Conda version": "2.0.3", + "EDAM operation (no superclasses)": [ + "Nucleic acid feature detection", + "Sequence motif recognition", + "Protein feature detection", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Functional genomics", + "Mobile genetic elements", + "Molecular biology", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "intermine_galaxy_exchange", + "Galaxy tool ids": [ + "galaxy_intermine_exchange" + ], + "Description": "InterMine Exporter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "intermine_galaxy_exchange", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange", + "Galaxy wrapper version": "0.0.1", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "interproscan", + "Galaxy tool ids": [ + "interproscan" + ], + "Description": "Interproscan queries the interpro database and provides annotations.", + "bio.tool id": "interproscan_ebi", + "bio.tool ids": [ + "interproscan_ebi" + ], + "biii": null, + "bio.tool name": "InterProScan (EBI)", + "bio.tool description": "Scan sequences against the InterPro protein signature databases.", + "EDAM operation": [ + "Sequence motif recognition", + "Protein feature detection" + ], + "EDAM topic": [ + "Gene and protein families", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.ebi.ac.uk/Tools/pfa/iprscan5/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "interproscan", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan", + "Galaxy wrapper version": "5.59-91.0", + "Conda id": "interproscan", + "Conda version": "5.59_91.0", + "EDAM operation (no superclasses)": [ + "Sequence motif recognition", + "Protein feature detection" + ], + "EDAM topic (no superclasses)": [ + "Gene and protein families", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "interval2maf", + "Galaxy tool ids": [ + "Interval2Maf1" + ], + "Description": "Extract MAF blocks given a set of intervals", + "bio.tool id": "bx-python", + "bio.tool ids": [ + "bx-python" + ], + "biii": null, + "bio.tool name": "bx-python", + "bio.tool description": "Tools for manipulating biological data, particularly multiple sequence alignments.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "interval2maf", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf", + "Galaxy wrapper version": "1.0.1+galaxy1", + "Conda id": "bx-python", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "intervene", + "Galaxy tool ids": [ + "intervene_pairwise", + "intervene_upset" + ], + "Description": "Create pairwise and upset plots", + "bio.tool id": "intervene", + "bio.tool ids": [ + "intervene" + ], + "biii": null, + "bio.tool name": "Intervene", + "bio.tool description": "Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.", + "EDAM operation": [ + "Sequence comparison", + "Sequence visualisation" + ], + "EDAM topic": [ + "Computational biology" + ], + "Status": "Up-to-date", + "Source": "https://intervene.readthedocs.io", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "intervene", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene", + "Galaxy wrapper version": "0.6.5", + "Conda id": "intervene", + "Conda version": "0.6.5", + "EDAM operation (no superclasses)": [ + "Sequence comparison", + "Sequence visualisation" + ], + "EDAM topic (no superclasses)": [ + "Computational biology" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "iqtree", + "Galaxy tool ids": [ + "iqtree" + ], + "Description": "Efficient phylogenomic software by maximum likelihood", + "bio.tool id": "iqtree", + "bio.tool ids": [ + "iqtree" + ], + "biii": null, + "bio.tool name": "iqtree", + "bio.tool description": "A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time", + "EDAM operation": [ + "Phylogenetic analysis", + "Sequence analysis" + ], + "EDAM topic": [ + "Phylogenetics" + ], + "Status": "Up-to-date", + "Source": "http://www.iqtree.org/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "iqtree", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree", + "Galaxy wrapper version": "2.3.4", + "Conda id": "iqtree", + "Conda version": "2.3.4", + "EDAM operation (no superclasses)": [ + "Phylogenetic analysis", + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "irissv", + "Galaxy tool ids": [ + "irissv" + ], + "Description": "Refine insertion sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/mkirsche/Iris", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "irissv", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/irissv/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv", + "Galaxy wrapper version": "1.0.5", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "isescan", + "Galaxy tool ids": [ + "isescan" + ], + "Description": "\"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.\"", + "bio.tool id": "ISEScan", + "bio.tool ids": [ + "ISEScan" + ], + "biii": null, + "bio.tool name": "ISEScan", + "bio.tool description": "Automated identification of insertion sequence elements in prokaryotic genomes.", + "EDAM operation": [ + "Structural variation detection" + ], + "EDAM topic": [ + "Genomics", + "DNA structural variation", + "Sequence analysis", + "Genetic variation" + ], + "Status": "To update", + "Source": "https://github.com/xiezhq/ISEScan", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ISEScan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan", + "Galaxy wrapper version": "1.7.2.3", + "Conda id": "isescan", + "Conda version": "1.7.2.1", + "EDAM operation (no superclasses)": [ + "Structural variation detection" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence analysis", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "isoformswitchanalyzer", + "Galaxy tool ids": [ + "isoformswitchanalyzer" + ], + "Description": "Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.", + "bio.tool id": "IsoformSwitchAnalyzeR", + "bio.tool ids": [ + "IsoformSwitchAnalyzeR" + ], + "biii": null, + "bio.tool name": "IsoformSwitchAnalyzeR", + "bio.tool description": "Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.", + "EDAM operation": [ + "Sequence comparison", + "Sequence analysis" + ], + "EDAM topic": [ + "Computational biology", + "Gene transcripts" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "isoformswitchanalyzer", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer", + "Galaxy wrapper version": "1.20.0", + "Conda id": "bioconductor-isoformswitchanalyzer", + "Conda version": "2.2.0", + "EDAM operation (no superclasses)": [ + "Sequence comparison", + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Computational biology", + "Gene transcripts" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ivar", + "Galaxy tool ids": [ + "ivar_consensus", + "ivar_filtervariants", + "ivar_removereads", + "ivar_trim", + "ivar_variants" + ], + "Description": "iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/andersen-lab/ivar", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ivar", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar", + "Galaxy wrapper version": "1.4.2", + "Conda id": "ivar", + "Conda version": "1.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "iwtomics", + "Galaxy tool ids": [ + "iwtomics_loadandplot", + "iwtomics_plotwithscale", + "iwtomics_testandplot" + ], + "Description": "Interval-Wise Testing for Omics Data", + "bio.tool id": "iwtomics", + "bio.tool ids": [ + "iwtomics" + ], + "biii": null, + "bio.tool name": "IWTomics", + "bio.tool description": "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in \"Omics\" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.", + "EDAM operation": [ + "Differential gene expression analysis", + "Differentially-methylated region identification", + "Peak calling", + "Genome annotation", + "Comparison" + ], + "EDAM topic": [ + "Statistics and probability" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/IWTomics.html", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "iwtomics", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics", + "Galaxy wrapper version": "1.0.0", + "Conda id": "bioconductor-iwtomics", + "Conda version": "1.26.0", + "EDAM operation (no superclasses)": [ + "Differential gene expression analysis", + "Peak calling", + "Genome annotation", + "Comparison" + ], + "EDAM topic (no superclasses)": [ + "Statistics and probability" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "jasminesv", + "Galaxy tool ids": [ + "jasminesv" + ], + "Description": "Merge structural variants across samples", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/mkirsche/Jasmine/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "jasminesv", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/jasminesv/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv", + "Galaxy wrapper version": "1.0.11", + "Conda id": "jasminesv", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "jbrowse", + "Galaxy tool ids": [ + "jbrowse_to_standalone", + "jbrowse" + ], + "Description": "JBrowse Genome Browser integrated as a Galaxy Tool", + "bio.tool id": "jbrowse", + "bio.tool ids": [ + "jbrowse" + ], + "biii": null, + "bio.tool name": "JBrowse", + "bio.tool description": "Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.", + "EDAM operation": [ + "Genome visualisation" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://jbrowse.org", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "jbrowse", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse", + "Galaxy wrapper version": "1.16.11", + "Conda id": "jbrowse", + "Conda version": "1.16.11", + "EDAM operation (no superclasses)": [ + "Genome visualisation" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "jcvi_gff_stats", + "Galaxy tool ids": [ + "jcvi_gff_stats" + ], + "Description": "Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/tanghaibao/jcvi", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "jcvi_gff_stats", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats", + "Galaxy wrapper version": "0.8.4", + "Conda id": "jcvi", + "Conda version": "1.4.15", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "jellyfish", + "Galaxy tool ids": [ + "jellyfish" + ], + "Description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA", + "bio.tool id": "Jellyfish", + "bio.tool ids": [ + "Jellyfish" + ], + "biii": null, + "bio.tool name": "Jellyfish", + "bio.tool description": "A command-line algorithm for counting k-mers in DNA sequence.", + "EDAM operation": [ + "k-mer counting" + ], + "EDAM topic": [ + "Sequence analysis", + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/gmarcais/Jellyfish", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "jellyfish", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish", + "Galaxy wrapper version": null, + "Conda id": "kmer-jellyfish", + "Conda version": "2.3.1", + "EDAM operation (no superclasses)": [ + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "join_files_by_id", + "Galaxy tool ids": [ + "join_files_by_id" + ], + "Description": "This tool will join datasets according to a column with identifier", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "join_files_by_id", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id", + "Galaxy wrapper version": "1.0", + "Conda id": "r-data.table", + "Conda version": "1.11.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "jq", + "Galaxy tool ids": [ + "jq" + ], + "Description": "JQ is a lightweight and flexible command-line JSON processor", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://stedolan.github.io/jq/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "jq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq", + "Galaxy wrapper version": "1.0", + "Conda id": "jq", + "Conda version": "1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "jvarkit", + "Galaxy tool ids": [ + "jvarkit_wgscoverageplotter" + ], + "Description": "Jvarkit : Java utilities for Bioinformatics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://lindenb.github.io/jvarkit/", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "jvarkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit", + "Galaxy wrapper version": "20201223", + "Conda id": "jvarkit-wgscoverageplotter", + "Conda version": "20201223", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "kallisto", + "Galaxy tool ids": [ + "kallisto_pseudo", + "kallisto_quant" + ], + "Description": "kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.", + "bio.tool id": "kallisto", + "bio.tool ids": [ + "kallisto" + ], + "biii": null, + "bio.tool name": "kallisto", + "bio.tool description": "A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.", + "EDAM operation": [ + "Gene expression profiling" + ], + "EDAM topic": [ + "Transcriptomics", + "RNA-seq", + "Gene expression" + ], + "Status": "To update", + "Source": "https://pachterlab.github.io/kallisto/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto", + "Galaxy wrapper version": "0.48.0", + "Conda id": "kallisto", + "Conda version": "0.50.1", + "EDAM operation (no superclasses)": [ + "Gene expression profiling" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "kc-align", + "Galaxy tool ids": [ + "kc-align" + ], + "Description": "Kc-Align custom tool", + "bio.tool id": "kc-align", + "bio.tool ids": [ + "kc-align" + ], + "biii": null, + "bio.tool name": "kc-align", + "bio.tool description": "A fast and accurate tool for performing codon-aware multiple sequence alignments", + "EDAM operation": [ + "Multiple sequence alignment" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/davebx/kc-align", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "kc_align", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align", + "Galaxy wrapper version": "1.0.2", + "Conda id": "kcalign", + "Conda version": "1.0.2", + "EDAM operation (no superclasses)": [ + "Multiple sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "khmer", + "Galaxy tool ids": [ + "khmer_abundance_distribution_single", + "khmer_abundance_distribution", + "khmer_count_median", + "khmer_partition", + "khmer_extract_partitions", + "khmer_filter_abundance", + "khmer_filter_below_abundance_cutoff", + "khmer_normalize_by_median" + ], + "Description": "In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more", + "bio.tool id": "khmer", + "bio.tool ids": [ + "khmer" + ], + "biii": null, + "bio.tool name": "khmer", + "bio.tool description": "khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.", + "EDAM operation": [ + "Standardisation and normalisation", + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://khmer.readthedocs.org/", + "ToolShed categories": [ + "Assembly", + "Next Gen Mappers" + ], + "ToolShed id": "khmer", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer", + "Galaxy wrapper version": "3.0.0a3", + "Conda id": "khmer", + "Conda version": "3.0.0a3", + "EDAM operation (no superclasses)": [ + "Standardisation and normalisation", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 8, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "king", + "Galaxy tool ids": [ + "king" + ], + "Description": "Kinship-based INference for Gwas", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://people.virginia.edu/~wc9c/KING/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "king", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/king", + "Galaxy wrapper version": "2.2.7", + "Conda id": "king", + "Conda version": "2.2.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "kleborate", + "Galaxy tool ids": [ + "kleborate" + ], + "Description": "Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)", + "bio.tool id": "kleborate", + "bio.tool ids": [ + "kleborate" + ], + "biii": null, + "bio.tool name": "Kleborate", + "bio.tool description": "Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).", + "EDAM operation": [ + "Multilocus sequence typing", + "Genome assembly", + "Virulence prediction" + ], + "EDAM topic": [ + "Public health and epidemiology", + "Metagenomics", + "Population genomics", + "Sequence assembly", + "Whole genome sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/katholt/Kleborate/wiki", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kleborate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/katholt/Kleborate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate", + "Galaxy wrapper version": "2.3.2", + "Conda id": "kleborate", + "Conda version": "2.3.2", + "EDAM operation (no superclasses)": [ + "Multilocus sequence typing", + "Genome assembly", + "Virulence prediction" + ], + "EDAM topic (no superclasses)": [ + "Public health and epidemiology", + "Metagenomics", + "Population genomics", + "Sequence assembly", + "Whole genome sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "kma", + "Galaxy tool ids": [ + "kma_map" + ], + "Description": "Map with KMA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/genomicepidemiology/kma", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "kma", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma", + "Galaxy wrapper version": "1.2.21", + "Conda id": "kma", + "Conda version": "1.4.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "kofamscan", + "Galaxy tool ids": [ + "kofamscan" + ], + "Description": "Gene function annotation tool based on KEGG Orthology and hidden Markov model", + "bio.tool id": "kofamscan", + "bio.tool ids": [ + "kofamscan" + ], + "biii": null, + "bio.tool name": "kofamscan", + "bio.tool description": "KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.", + "EDAM operation": [ + "Sequence analysis", + "Gene functional annotation" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/takaram/kofam_scan", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "kofamscan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan", + "Galaxy wrapper version": "1.3.0", + "Conda id": "kofamscan", + "Conda version": "1.3.0", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Gene functional annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "kraken_biom", + "Galaxy tool ids": [ + "kraken_biom" + ], + "Description": "Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/smdabdoub/kraken-biom", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kraken_biom", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/smdabdoub/kraken-biom", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom", + "Galaxy wrapper version": "1.2.0", + "Conda id": "kraken-biom", + "Conda version": "1.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "kraken_taxonomy_report", + "Galaxy tool ids": [ + "kraken_taxonomy_report" + ], + "Description": "Kraken taxonomy report", + "bio.tool id": "Kraken-Taxonomy-Report", + "bio.tool ids": [ + "Kraken-Taxonomy-Report" + ], + "biii": null, + "bio.tool name": "Kraken-Taxonomy-Report", + "bio.tool description": "view report of classification for multiple samples", + "EDAM operation": [ + "Visualisation", + "Classification" + ], + "EDAM topic": [ + "Metagenomics", + "Taxonomy" + ], + "Status": "To update", + "Source": "https://github.com/blankenberg/Kraken-Taxonomy-Report", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kraken_taxonomy_report", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report", + "Galaxy wrapper version": "0.0.3", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [ + "Visualisation", + "Classification" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Taxonomy" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "krakentools", + "Galaxy tool ids": [ + "krakentools_alpha_diversity", + "krakentools_beta_diversity", + "krakentools_combine_kreports", + "krakentools_extract_kraken_reads", + "krakentools_kreport2krona", + "krakentools_kreport2mpa" + ], + "Description": "KrakenTools is a suite of scripts to be used alongside the Kraken", + "bio.tool id": "krakentools", + "bio.tool ids": [ + "krakentools" + ], + "biii": null, + "bio.tool name": "KrakenTools", + "bio.tool description": "KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files", + "EDAM operation": [ + "Visualisation", + "Aggregation" + ], + "EDAM topic": [ + "Taxonomy", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/jenniferlu717/KrakenTools", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "krakentools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools", + "Galaxy wrapper version": "1.2", + "Conda id": "krakentools", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [ + "Visualisation", + "Aggregation" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy", + "Metagenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 6 + }, + { + "Galaxy wrapper id": "krocus", + "Galaxy tool ids": [ + "krocus" + ], + "Description": "Predict MLST directly from uncorrected long reads", + "bio.tool id": "krocus", + "bio.tool ids": [ + "krocus" + ], + "biii": null, + "bio.tool name": "krocus", + "bio.tool description": "Predict MLST directly from uncorrected long reads", + "EDAM operation": [ + "Multilocus sequence typing", + "k-mer counting" + ], + "EDAM topic": [ + "Public health and epidemiology" + ], + "Status": "To update", + "Source": "https://github.com/quadram-institute-bioscience/krocus", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "krocus", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus", + "Galaxy wrapper version": "1.0.1", + "Conda id": "krocus", + "Conda version": "1.0.3", + "EDAM operation (no superclasses)": [ + "Multilocus sequence typing", + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Public health and epidemiology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "last", + "Galaxy tool ids": [ + "last_al", + "last_db", + "last_split", + "last_train", + "last_maf_convert" + ], + "Description": "LAST finds similar regions between sequences.", + "bio.tool id": "last", + "bio.tool ids": [ + "last" + ], + "biii": null, + "bio.tool name": "LAST", + "bio.tool description": "Short read alignment program incorporating quality scores", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "Genomics", + "Comparative genomics" + ], + "Status": "To update", + "Source": "http://last.cbrc.jp/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "last", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/last", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/last", + "Galaxy wrapper version": "1205", + "Conda id": "last", + "Conda version": "1542", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Comparative genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "lastz", + "Galaxy tool ids": [ + "lastz_wrapper_2", + "lastz_d_wrapper" + ], + "Description": "Galaxy wrappers for the Lastz and Lastz_d", + "bio.tool id": "lastz", + "bio.tool ids": [ + "lastz" + ], + "biii": null, + "bio.tool name": "LASTZ", + "bio.tool description": "A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.", + "EDAM operation": [ + "Sequence alignment", + "Read mapping" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lastz/lastz", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "lastz", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz", + "Galaxy wrapper version": "1.04.22", + "Conda id": "lastz", + "Conda version": "1.04.22", + "EDAM operation (no superclasses)": [ + "Sequence alignment", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "lcrgenie", + "Galaxy tool ids": [ + "lcrgenie" + ], + "Description": "Ligase Chain Reaction Genie", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/neilswainston/LCRGenie", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "lcrgenie", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie", + "Galaxy wrapper version": "1.0.2", + "Conda id": "lcr_genie", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "legsta", + "Galaxy tool ids": [ + "legsta" + ], + "Description": "Performs in silico Legionella pneumophila sequence based typing.", + "bio.tool id": "legsta", + "bio.tool ids": [ + "legsta" + ], + "biii": null, + "bio.tool name": "legsta", + "bio.tool description": "Performs in silico Legionella pneumophila sequence based typing", + "EDAM operation": [ + "Sequence analysis" + ], + "EDAM topic": [ + "Public health and epidemiology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/legsta", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "legsta", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/tseemann/legsta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta", + "Galaxy wrapper version": "0.5.1", + "Conda id": "legsta", + "Conda version": "0.5.1", + "EDAM operation (no superclasses)": [ + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Public health and epidemiology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "length_and_gc_content", + "Galaxy tool ids": [ + "length_and_gc_content" + ], + "Description": "Gets gene length and gc content from a fasta and a GTF file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content", + "ToolShed categories": [ + "Fasta Manipulation", + "Statistics", + "RNA", + "Micro-array Analysis" + ], + "ToolShed id": "length_and_gc_content", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content", + "Galaxy wrapper version": "0.1.2", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "limma_voom", + "Galaxy tool ids": [ + "limma_voom" + ], + "Description": "Perform RNA-Seq differential expression analysis using limma voom pipeline", + "bio.tool id": "limma", + "bio.tool ids": [ + "limma" + ], + "biii": null, + "bio.tool name": "limma", + "bio.tool description": "Data analysis, linear models and differential expression for microarray data.", + "EDAM operation": [ + "RNA-Seq analysis" + ], + "EDAM topic": [ + "Molecular biology", + "Genetics" + ], + "Status": "Up-to-date", + "Source": "http://bioconductor.org/packages/release/bioc/html/limma.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "limma_voom", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom", + "Galaxy wrapper version": "3.58.1", + "Conda id": "bioconductor-limma", + "Conda version": "3.58.1", + "EDAM operation (no superclasses)": [ + "RNA-Seq analysis" + ], + "EDAM topic (no superclasses)": [ + "Molecular biology", + "Genetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "lineagespot", + "Galaxy tool ids": [ + "lineagespot" + ], + "Description": "Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)", + "bio.tool id": "lineagespot", + "bio.tool ids": [ + "lineagespot" + ], + "biii": null, + "bio.tool name": "lineagespot", + "bio.tool description": "Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).", + "EDAM operation": [ + "Variant calling" + ], + "EDAM topic": [ + "Metagenomics", + "Gene transcripts", + "Evolutionary biology", + "Sequencing", + "Genetic variation" + ], + "Status": "To update", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html", + "ToolShed categories": [ + "Metagenomics", + "Sequence Analysis" + ], + "ToolShed id": "lineagespot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot", + "Galaxy wrapper version": "1.6.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Gene transcripts", + "Evolutionary biology", + "Sequencing", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "links", + "Galaxy tool ids": [ + "links" + ], + "Description": "Scaffold genome assemblies with long reads.", + "bio.tool id": "links", + "bio.tool ids": [ + "links" + ], + "biii": null, + "bio.tool name": "LINKS", + "bio.tool description": "LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.", + "EDAM operation": [ + "Scaffolding", + "Genome assembly", + "Read mapping", + "Read pre-processing", + "Sequence trimming" + ], + "EDAM topic": [ + "Sequence assembly", + "Mapping", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/bcgsc/LINKS", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "links", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/links", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/links", + "Galaxy wrapper version": "2.0.1", + "Conda id": "links", + "Conda version": "2.0.1", + "EDAM operation (no superclasses)": [ + "Scaffolding", + "Genome assembly", + "Read mapping", + "Read pre-processing", + "Sequence trimming" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Mapping", + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "lofreq", + "Galaxy tool ids": [ + "lofreq_alnqual", + "lofreq_call", + "lofreq_filter", + "lofreq_indelqual", + "lofreq_viterbi" + ], + "Description": "LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csb5.github.io/lofreq/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq", + "Galaxy wrapper version": "2.1.5", + "Conda id": "lofreq", + "Conda version": "2.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "lorikeet", + "Galaxy tool ids": [ + "lorikeet_spoligotype" + ], + "Description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", + "bio.tool id": "lorikeet", + "bio.tool ids": [ + "lorikeet" + ], + "biii": null, + "bio.tool name": "lorikeet", + "bio.tool description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", + "EDAM operation": [ + "Sequence analysis", + "Genotyping" + ], + "EDAM topic": [ + "Genotype and phenotype" + ], + "Status": "Up-to-date", + "Source": "https://github.com/AbeelLab/lorikeet", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "lorikeet_spoligotype", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/AbeelLab/lorikeet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet", + "Galaxy wrapper version": "20", + "Conda id": "lorikeet", + "Conda version": "20", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Genotyping" + ], + "EDAM topic (no superclasses)": [ + "Genotype and phenotype" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "lumpy_sv", + "Galaxy tool ids": [ + "lumpy_prep", + "lumpy_sv" + ], + "Description": "LUMPY - a general probabilistic framework for structural variant discovery", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://layerlab.org/software/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "lumpy_sv", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/arq5x/lumpy-sv", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv", + "Galaxy wrapper version": "0.3.1", + "Conda id": "lumpy-sv", + "Conda version": "0.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "m6anet", + "Galaxy tool ids": [ + "m6anet" + ], + "Description": "m6anet to detect m6A RNA modifications from nanopore data", + "bio.tool id": "m6Anet", + "bio.tool ids": [ + "m6Anet" + ], + "biii": null, + "bio.tool name": "m6Anet", + "bio.tool description": "Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.", + "EDAM operation": [ + "Quantification", + "Imputation", + "Gene expression profiling" + ], + "EDAM topic": [ + "RNA-Seq", + "Transcriptomics", + "RNA", + "Machine learning" + ], + "Status": "Up-to-date", + "Source": "https://m6anet.readthedocs.io/en/latest", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "m6anet", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet", + "Galaxy wrapper version": "2.1.0", + "Conda id": "m6anet", + "Conda version": "2.1.0", + "EDAM operation (no superclasses)": [ + "Quantification", + "Imputation", + "Gene expression profiling" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Transcriptomics", + "RNA", + "Machine learning" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "maaslin2", + "Galaxy tool ids": [ + "maaslin2" + ], + "Description": "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.", + "bio.tool id": "maaslin2", + "bio.tool ids": [ + "maaslin2" + ], + "biii": null, + "bio.tool name": "MaAsLin2", + "bio.tool description": "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.", + "EDAM operation": [ + "Filtering", + "Statistical calculation", + "Standardisation and normalisation", + "Visualisation" + ], + "EDAM topic": [ + "Metagenomics", + "Statistics and probability" + ], + "Status": "To update", + "Source": "http://huttenhower.sph.harvard.edu/maaslin", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "maaslin2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/biobakery/Maaslin2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2", + "Galaxy wrapper version": "0.99.12", + "Conda id": "maaslin2", + "Conda version": "1.16.0", + "EDAM operation (no superclasses)": [ + "Filtering", + "Standardisation and normalisation", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "macs2", + "Galaxy tool ids": [ + "macs2_bdgbroadcall", + "macs2_bdgcmp", + "macs2_bdgdiff", + "macs2_bdgpeakcall", + "macs2_callpeak", + "macs2_filterdup", + "macs2_predictd", + "macs2_randsample", + "macs2_refinepeak" + ], + "Description": "MACS - Model-based Analysis of ChIP-Seq", + "bio.tool id": "macs", + "bio.tool ids": [ + "macs" + ], + "biii": null, + "bio.tool name": "MACS", + "bio.tool description": "Model-based Analysis of ChIP-seq data.", + "EDAM operation": [ + "Peak calling", + "Enrichment analysis", + "Gene regulatory network analysis" + ], + "EDAM topic": [ + "ChIP-seq", + "Molecular interactions, pathways and networks", + "Transcription factors and regulatory sites" + ], + "Status": "Up-to-date", + "Source": "https://github.com/taoliu/MACS", + "ToolShed categories": [ + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": "macs2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2", + "Galaxy wrapper version": "2.2.9.1", + "Conda id": "macs2", + "Conda version": "2.2.9.1", + "EDAM operation (no superclasses)": [ + "Peak calling", + "Enrichment analysis", + "Gene regulatory network analysis" + ], + "EDAM topic (no superclasses)": [ + "ChIP-seq", + "Molecular interactions, pathways and networks", + "Transcription factors and regulatory sites" + ], + "Available on UseGalaxy.org": 9, + "Available on UseGalaxy.org.au": 9, + "Available on UseGalaxy.eu": 9, + "Available on UseGalaxy.org.fr": 9 + }, + { + "Galaxy wrapper id": "maf_stats", + "Galaxy tool ids": [ + "maf_stats1" + ], + "Description": "MAF Coverage statistics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "maf_stats", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats", + "Galaxy wrapper version": "1.0.2+galaxy0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "mageck", + "Galaxy tool ids": [ + "mageck_count", + "mageck_gsea", + "mageck_mle", + "mageck_pathway", + "mageck_test" + ], + "Description": "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.", + "bio.tool id": "mageck", + "bio.tool ids": [ + "mageck" + ], + "biii": null, + "bio.tool name": "MAGeCK", + "bio.tool description": "Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.", + "EDAM operation": [ + "Genetic variation analysis" + ], + "EDAM topic": [ + "Genetics", + "Genetic variation", + "Genomics" + ], + "Status": "To update", + "Source": "https://sourceforge.net/projects/mageck/", + "ToolShed categories": [ + "Genome editing" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck", + "Galaxy wrapper version": "0.5.9.2", + "Conda id": "mageck", + "Conda version": "0.5.9.5", + "EDAM operation (no superclasses)": [ + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Genetics", + "Genetic variation", + "Genomics" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "maker", + "Galaxy tool ids": [ + "maker", + "maker_map_ids" + ], + "Description": "MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.", + "bio.tool id": "maker", + "bio.tool ids": [ + "maker" + ], + "biii": null, + "bio.tool name": "MAKER", + "bio.tool description": "Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Genomics", + "DNA", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.yandell-lab.org/software/maker.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker", + "Galaxy wrapper version": "2.31.11", + "Conda id": "maker", + "Conda version": "3.01.03", + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "DNA", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "malt", + "Galaxy tool ids": [ + "malt_run" + ], + "Description": "Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/husonlab/malt", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "malt_run", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt", + "Galaxy wrapper version": "0.5.3", + "Conda id": "malt", + "Conda version": "0.62", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "map_param_value", + "Galaxy tool ids": [ + "map_param_value" + ], + "Description": "Map a parameter value to another value", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "map_param_value", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value", + "Galaxy wrapper version": "0.2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mapseq", + "Galaxy tool ids": [ + "mapseq" + ], + "Description": "fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.", + "bio.tool id": "mapseq", + "bio.tool ids": [ + "mapseq" + ], + "biii": null, + "bio.tool name": "MAPseq", + "bio.tool description": "Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .", + "EDAM operation": [ + "k-mer counting" + ], + "EDAM topic": [ + "Functional, regulatory and non-coding RNA", + "Sequence analysis", + "Sequence sites, features and motifs" + ], + "Status": "To update", + "Source": "https://github.com/jfmrod/MAPseq", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "mapseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq", + "Galaxy wrapper version": "2.1.1", + "Conda id": "perl", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Functional, regulatory and non-coding RNA", + "Sequence analysis", + "Sequence sites, features and motifs" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mash", + "Galaxy tool ids": [ + "mash_screen", + "mash_sketch" + ], + "Description": "Fast genome and metagenome distance estimation using MinHash", + "bio.tool id": "mash", + "bio.tool ids": [ + "mash" + ], + "biii": null, + "bio.tool name": "Mash", + "bio.tool description": "Fast genome and metagenome distance estimation using MinHash.", + "EDAM operation": [ + "Sequence distance matrix generation" + ], + "EDAM topic": [ + "Genomics", + "Metagenomics", + "Statistics and probability", + "Sequence analysis", + "DNA mutation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/Mash", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash", + "Galaxy wrapper version": "2.3", + "Conda id": "mash", + "Conda version": "2.3", + "EDAM operation (no superclasses)": [ + "Sequence distance matrix generation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Statistics and probability", + "Sequence analysis", + "DNA mutation" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "mashmap", + "Galaxy tool ids": [ + "mashmap" + ], + "Description": "Fast local alignment boundaries", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mashmap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap", + "Galaxy wrapper version": "3.1.3", + "Conda id": "mashmap", + "Conda version": "3.1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "masigpro", + "Galaxy tool ids": [ + "masigpro" + ], + "Description": "Identify significantly differential expression profiles in time-course microarray experiments", + "bio.tool id": "masigpro", + "bio.tool ids": [ + "masigpro" + ], + "biii": null, + "bio.tool name": "maSigPro", + "bio.tool description": "Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.", + "EDAM operation": [ + "Regression analysis" + ], + "EDAM topic": [ + "Gene expression", + "Molecular genetics", + "Microarray experiment", + "RNA-Seq" + ], + "Status": "To update", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "masigpro", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro", + "Galaxy wrapper version": "1.49.3", + "Conda id": "coreutils", + "Conda version": "8.25", + "EDAM operation (no superclasses)": [ + "Regression analysis" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "Microarray experiment", + "RNA-Seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "maxbin2", + "Galaxy tool ids": [ + "maxbin2" + ], + "Description": "clusters metagenomic contigs into bins", + "bio.tool id": "maxbin", + "bio.tool ids": [ + "maxbin" + ], + "biii": null, + "bio.tool name": "MaxBin", + "bio.tool description": "Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.", + "EDAM operation": [ + "Sequence assembly" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence assembly", + "Microbiology" + ], + "Status": "To update", + "Source": "https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "maxbin2", + "Galaxy wrapper owner": "mbernt", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2", + "Galaxy wrapper version": null, + "Conda id": "maxbin2", + "Conda version": "2.2.7", + "EDAM operation (no superclasses)": [ + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence assembly", + "Microbiology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "mcl", + "Galaxy tool ids": [ + "mcl" + ], + "Description": "The Markov Cluster Algorithm, a cluster algorithm for graphs", + "bio.tool id": "mcl", + "bio.tool ids": [ + "mcl" + ], + "biii": null, + "bio.tool name": "MCL", + "bio.tool description": "MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.", + "EDAM operation": [ + "Clustering", + "Network analysis", + "Gene regulatory network analysis" + ], + "EDAM topic": [ + "Molecular interactions, pathways and networks" + ], + "Status": "Up-to-date", + "Source": "https://micans.org/mcl/man/mcl.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mcl", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/mcl", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl", + "Galaxy wrapper version": "22.282", + "Conda id": "mcl", + "Conda version": "22.282", + "EDAM operation (no superclasses)": [ + "Clustering", + "Gene regulatory network analysis" + ], + "EDAM topic (no superclasses)": [ + "Molecular interactions, pathways and networks" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "medaka", + "Galaxy tool ids": [ + "medaka_consensus", + "medaka_consensus_pipeline", + "medaka_snp", + "medaka_variant" + ], + "Description": "Sequence correction provided by ONT Research", + "bio.tool id": "medaka", + "bio.tool ids": [ + "medaka" + ], + "biii": null, + "bio.tool name": "Medaka", + "bio.tool description": "medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.", + "EDAM operation": [ + "Base-calling", + "Variant calling", + "Sequence assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Machine learning" + ], + "Status": "To update", + "Source": "https://github.com/nanoporetech/medaka", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka", + "Galaxy wrapper version": "1.7.2", + "Conda id": "medaka", + "Conda version": "1.11.3", + "EDAM operation (no superclasses)": [ + "Base-calling", + "Variant calling", + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Machine learning" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "megahit", + "Galaxy tool ids": [ + "megahit" + ], + "Description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.", + "bio.tool id": "megahit", + "bio.tool ids": [ + "megahit" + ], + "biii": null, + "bio.tool name": "MEGAHIT", + "bio.tool description": "Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Metagenomics", + "Sequencing", + "Ecology", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/voutcn/megahit", + "ToolShed categories": [ + "Sequence Analysis", + "Assembly", + "Metagenomics" + ], + "ToolShed id": "megahit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit", + "Galaxy wrapper version": "1.2.9", + "Conda id": "megahit", + "Conda version": "1.2.9", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "megahit_contig2fastg", + "Galaxy tool ids": [ + "megahit_contig2fastg" + ], + "Description": "A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)", + "bio.tool id": "megahit", + "bio.tool ids": [ + "megahit" + ], + "biii": null, + "bio.tool name": "MEGAHIT", + "bio.tool description": "Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Metagenomics", + "Sequencing", + "Ecology", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp", + "ToolShed categories": [ + "Sequence Analysis", + "Assembly", + "Metagenomics" + ], + "ToolShed id": "megahit_contig2fastg", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg", + "Galaxy wrapper version": "1.1.3", + "Conda id": "megahit", + "Conda version": "1.2.9", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "megan", + "Galaxy tool ids": [ + "megan_blast2lca", + "megan_blast2rma", + "megan_daa2info", + "megan_daa2rma", + "megan_daa_meganizer", + "megan_read_extractor", + "megan_sam2rma" + ], + "Description": "MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).", + "bio.tool id": "megan", + "bio.tool ids": [ + "megan" + ], + "biii": null, + "bio.tool name": "MEGAN", + "bio.tool description": "Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.", + "EDAM operation": [ + "Sequence analysis", + "Taxonomic classification" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/husonlab/megan-ce", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "megan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan", + "Galaxy wrapper version": "6.21.7", + "Conda id": "megan", + "Conda version": "6.25.9", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "meme", + "Galaxy tool ids": [ + "meme_dreme", + "meme_fimo", + "meme_meme", + "meme_psp_gen" + ], + "Description": "The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.", + "bio.tool id": "meme_meme", + "bio.tool ids": [ + "meme_meme", + "meme_fimo" + ], + "biii": null, + "bio.tool name": "meme_meme", + "bio.tool description": "An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.", + "EDAM operation": [ + "Nucleic acid feature detection", + "Protein feature detection", + "Statistical calculation" + ], + "EDAM topic": [ + "Data mining", + "Sequence analysis", + "Genetic variation", + "Statistics and probability" + ], + "Status": "To update", + "Source": "http://meme-suite.org/", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "meme", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme", + "Galaxy wrapper version": "5.4.1", + "Conda id": "meme", + "Conda version": "5.5.5", + "EDAM operation (no superclasses)": [ + "Nucleic acid feature detection", + "Protein feature detection", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Data mining", + "Sequence analysis", + "Genetic variation", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "meme_chip", + "Galaxy tool ids": [ + "meme_chip" + ], + "Description": "Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://meme-suite.org/", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "meme_chip", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip", + "Galaxy wrapper version": "4.11.2", + "Conda id": "graphicsmagick", + "Conda version": "1.3.26", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "meningotype", + "Galaxy tool ids": [ + "meningotype" + ], + "Description": "Assign sequence type to N. meningitidis genome assemblies", + "bio.tool id": "meningotype", + "bio.tool ids": [ + "meningotype" + ], + "biii": null, + "bio.tool name": "meningotype", + "bio.tool description": "In silico typing of Neisseria meningitidis contigs.", + "EDAM operation": [ + "Genotyping", + "Multilocus sequence typing" + ], + "EDAM topic": [ + "Microbiology", + "Genotype and phenotype" + ], + "Status": "Up-to-date", + "Source": "https://github.com/MDU-PHL/meningotype", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "meningotype", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype", + "Galaxy wrapper version": "0.8.5", + "Conda id": "meningotype", + "Conda version": "0.8.5", + "EDAM operation (no superclasses)": [ + "Multilocus sequence typing" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Genotype and phenotype" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "merlin", + "Galaxy tool ids": [ + "merlin" + ], + "Description": "Pedigree Analysis package", + "bio.tool id": "merlin", + "bio.tool ids": [ + "merlin" + ], + "biii": null, + "bio.tool name": "Merlin", + "bio.tool description": "Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation", + "EDAM operation": [ + "Haplotype mapping", + "Genetic mapping" + ], + "EDAM topic": [ + "GWAS study", + "Mapping" + ], + "Status": "Up-to-date", + "Source": "http://csg.sph.umich.edu/abecasis/Merlin/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "merlin", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin", + "Galaxy wrapper version": "1.1.2", + "Conda id": "merlin", + "Conda version": "1.1.2", + "EDAM operation (no superclasses)": [ + "Haplotype mapping" + ], + "EDAM topic (no superclasses)": [ + "GWAS study", + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "merqury", + "Galaxy tool ids": [ + "merqury", + "merquryplot" + ], + "Description": "Merqury is a tool for evaluating genomes assemblies based of k-mer operations.", + "bio.tool id": "merqury", + "bio.tool ids": [ + "merqury" + ], + "biii": null, + "bio.tool name": "Merqury", + "bio.tool description": "Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.", + "EDAM operation": [ + "Genome assembly", + "k-mer counting", + "Scaffolding", + "Phasing", + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly", + "Whole genome sequencing", + "Plant biology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/merqury", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "merqury", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury", + "Galaxy wrapper version": "1.3", + "Conda id": "merqury", + "Conda version": "1.3", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "k-mer counting", + "Scaffolding", + "Phasing", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Whole genome sequencing", + "Plant biology" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "meryl", + "Galaxy tool ids": [ + "meryl_arithmetic_kmers", + "meryl_count_kmers", + "meryl_filter_kmers", + "meryl_groups_kmers", + "meryl_histogram_kmers", + "meryl_print", + "meryl_trio_mode" + ], + "Description": "Meryl a k-mer counter.", + "bio.tool id": "meryl", + "bio.tool ids": [ + "meryl" + ], + "biii": null, + "bio.tool name": "Meryl", + "bio.tool description": "Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.", + "EDAM operation": [ + "k-mer counting" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Genomics", + "Sequence analysis", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/meryl", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "meryl", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl", + "Galaxy wrapper version": "1.3", + "Conda id": "merqury", + "Conda version": "1.3", + "EDAM operation (no superclasses)": [ + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Genomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metabat2", + "Galaxy tool ids": [ + "metabat2_jgi_summarize_bam_contig_depths", + "metabat2" + ], + "Description": "MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.", + "bio.tool id": "MetaBAT_2", + "bio.tool ids": [ + "MetaBAT_2" + ], + "biii": null, + "bio.tool name": "MetaBAT 2", + "bio.tool description": "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different \"bins\", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning", + "EDAM operation": [ + "Read binning", + "Sequence assembly", + "Genome annotation" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence assembly", + "Metagenomic sequencing" + ], + "Status": "Up-to-date", + "Source": "https://bitbucket.org/berkeleylab/metabat/src/master/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "metabat2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2", + "Galaxy wrapper version": "2.15", + "Conda id": "metabat2", + "Conda version": "2.15", + "EDAM operation (no superclasses)": [ + "Read binning", + "Sequence assembly", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence assembly", + "Metagenomic sequencing" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "metabuli", + "Galaxy tool ids": [ + "metabuli_classify" + ], + "Description": "Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences", + "bio.tool id": "metabuli", + "bio.tool ids": [ + "metabuli" + ], + "biii": null, + "bio.tool name": "metabuli", + "bio.tool description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", + "EDAM operation": [ + "Taxonomic classification" + ], + "EDAM topic": [ + "Taxonomy" + ], + "Status": "Up-to-date", + "Source": "https://github.com/steineggerlab/Metabuli", + "ToolShed categories": [ + "Sequence Analysis", + "Metagenomics" + ], + "ToolShed id": "metabuli", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli", + "Galaxy wrapper version": "1.0.5", + "Conda id": "metabuli", + "Conda version": "1.0.5", + "EDAM operation (no superclasses)": [ + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metaeuk", + "Galaxy tool ids": [ + "metaeuk_easy_predict" + ], + "Description": "MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. ", + "bio.tool id": "MetaEuk", + "bio.tool ids": [ + "MetaEuk" + ], + "biii": null, + "bio.tool name": "MetaEuk", + "bio.tool description": "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics", + "EDAM operation": [ + "Homology-based gene prediction" + ], + "EDAM topic": [ + "Metagenomics", + "Gene and protein families" + ], + "Status": "To update", + "Source": "https://github.com/soedinglab/metaeuk", + "ToolShed categories": [ + "Sequence Analysis", + "Genome annotation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk", + "Galaxy wrapper version": "5.34c21f2", + "Conda id": "metaeuk", + "Conda version": "6.a5d39d9", + "EDAM operation (no superclasses)": [ + "Homology-based gene prediction" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Gene and protein families" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metagenomeseq", + "Galaxy tool ids": [ + "metagenomeseq_normalizaton" + ], + "Description": "metagenomeSeq Normalization", + "bio.tool id": "metagenomeseq", + "bio.tool ids": [ + "metagenomeseq" + ], + "biii": null, + "bio.tool name": "metagenomeSeq", + "bio.tool description": "Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.", + "EDAM operation": [ + "Sequence visualisation", + "Statistical calculation" + ], + "EDAM topic": [ + "Metagenomics", + "Sequencing" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "metagenomeseq_normalization", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq", + "Galaxy wrapper version": "1.16.0-0.0.1", + "Conda id": "bioconductor-metagenomeseq", + "Conda version": "1.43.0", + "EDAM operation (no superclasses)": [ + "Sequence visualisation", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "metaphlan", + "Galaxy tool ids": [ + "customize_metaphlan_database", + "extract_metaphlan_database", + "merge_metaphlan_tables", + "metaphlan" + ], + "Description": "MetaPhlAn for Metagenomic Phylogenetic Analysis", + "bio.tool id": "metaphlan", + "bio.tool ids": [ + "metaphlan" + ], + "biii": null, + "bio.tool name": "MetaPhlAn", + "bio.tool description": "Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", + "EDAM operation": [ + "Nucleic acid sequence analysis", + "Phylogenetic tree analysis" + ], + "EDAM topic": [ + "Metagenomics", + "Phylogenomics" + ], + "Status": "To update", + "Source": "https://github.com/biobakery/MetaPhlAn", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "metaphlan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan", + "Galaxy wrapper version": "4.0.6", + "Conda id": "metaphlan", + "Conda version": "4.1.1", + "EDAM operation (no superclasses)": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Phylogenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "metawrapmg", + "Galaxy tool ids": [ + "metawrapmg_binning" + ], + "Description": "A flexible pipeline for genome-resolved metagenomic data analysis", + "bio.tool id": "metawrap", + "bio.tool ids": [ + "metawrap" + ], + "biii": null, + "bio.tool name": "MetaWRAP", + "bio.tool description": "MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.", + "EDAM operation": [ + "Read binning", + "Sequence assembly", + "Genome annotation", + "Sequence trimming", + "Demultiplexing" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Metagenomic sequencing", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/bxlab/metaWRAP", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "metawrapmg_binning", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg", + "Galaxy wrapper version": "1.3.0", + "Conda id": "metawrap-mg", + "Conda version": "1.3.0", + "EDAM operation (no superclasses)": [ + "Read binning", + "Sequence assembly", + "Genome annotation", + "Sequence trimming", + "Demultiplexing" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Metagenomic sequencing", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "migmap", + "Galaxy tool ids": [ + "migmap" + ], + "Description": "mapper for full-length T- and B-cell repertoire sequencing", + "bio.tool id": "MiGMAP", + "bio.tool ids": [ + "MiGMAP" + ], + "biii": null, + "bio.tool name": "MiGMAP", + "bio.tool description": "Mapper for full-length T- and B-cell repertoire sequencing.", + "EDAM operation": [ + "Sequence analysis", + "Read mapping" + ], + "EDAM topic": [ + "Immunoproteins, genes and antigens", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/mikessh/migmap", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "migmap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap", + "Galaxy wrapper version": "1.0.3", + "Conda id": "migmap", + "Conda version": "1.0.3", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "minia", + "Galaxy tool ids": [ + "minia" + ], + "Description": "Short-read assembler based on a de Bruijn graph", + "bio.tool id": "minia", + "bio.tool ids": [ + "minia" + ], + "biii": null, + "bio.tool name": "Minia", + "bio.tool description": "Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://gatb.inria.fr/software/minia/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "minia", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia", + "Galaxy wrapper version": "3.2.6", + "Conda id": "minia", + "Conda version": "3.2.6", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "miniasm", + "Galaxy tool ids": [ + "miniasm" + ], + "Description": "Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)", + "bio.tool id": "miniasm", + "bio.tool ids": [ + "miniasm" + ], + "biii": null, + "bio.tool name": "miniasm", + "bio.tool description": "Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.", + "EDAM operation": [ + "De-novo assembly" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/lh3/miniasm", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "miniasm", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm", + "Galaxy wrapper version": "0.3_r179", + "Conda id": "miniasm", + "Conda version": "0.3", + "EDAM operation (no superclasses)": [ + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "minimap2", + "Galaxy tool ids": [ + "minimap2" + ], + "Description": "A fast pairwise aligner for genomic and spliced nucleotide sequences", + "bio.tool id": "minimap2", + "bio.tool ids": [ + "minimap2" + ], + "biii": null, + "bio.tool name": "Minimap2", + "bio.tool description": "Pairwise aligner for genomic and spliced nucleotide sequences", + "EDAM operation": [ + "Pairwise sequence alignment" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lh3/minimap2", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "minimap2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2", + "Galaxy wrapper version": "2.28", + "Conda id": "minimap2", + "Conda version": "2.28", + "EDAM operation (no superclasses)": [ + "Pairwise sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "miniprot", + "Galaxy tool ids": [ + "miniprot", + "miniprot_index" + ], + "Description": "Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.", + "bio.tool id": "miniprot", + "bio.tool ids": [ + "miniprot" + ], + "biii": null, + "bio.tool name": "miniprot", + "bio.tool description": "Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.", + "EDAM operation": [ + "Sequence alignment", + "Protein sequence analysis" + ], + "EDAM topic": [ + "Sequence sites, features and motifs", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lh3/miniprot", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot", + "Galaxy wrapper version": "0.13", + "Conda id": "miniprot", + "Conda version": "0.13", + "EDAM operation (no superclasses)": [ + "Sequence alignment", + "Protein sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence sites, features and motifs", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "mirmachine", + "Galaxy tool ids": [ + "mirmachine" + ], + "Description": "Tool to detect miRNA in genome sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/sinanugur/MirMachine", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mirmachine", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine", + "Galaxy wrapper version": "0.2.13", + "Conda id": "mirmachine", + "Conda version": "0.2.13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mirnature", + "Galaxy tool ids": [ + "mirnature" + ], + "Description": "Computational detection of canonical microRNAs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/Bierinformatik/miRNAture", + "ToolShed categories": [ + "RNA", + "Sequence Analysis" + ], + "ToolShed id": "mirnature", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/Bierinformatik/miRNAture", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature", + "Galaxy wrapper version": "1.1", + "Conda id": "mirnature", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mitobim", + "Galaxy tool ids": [ + "mitobim" + ], + "Description": "assemble mitochondrial genomes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/chrishah/MITObim", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "mitobim", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim", + "Galaxy wrapper version": "1.9.1", + "Conda id": "mitobim", + "Conda version": "1.9.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mitos", + "Galaxy tool ids": [ + "mitos", + "mitos2" + ], + "Description": "de-novo annotation of metazoan mitochondrial genomes", + "bio.tool id": "mitos", + "bio.tool ids": [ + "mitos" + ], + "biii": null, + "bio.tool name": "MITOS", + "bio.tool description": "De novo metazoan mitochondrial genome annotation.", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Zoology", + "Whole genome sequencing" + ], + "Status": "To update", + "Source": "http://mitos.bioinf.uni-leipzig.de/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mitos", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos", + "Galaxy wrapper version": "1.1.7", + "Conda id": "mitos", + "Conda version": "2.1.9", + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Zoology", + "Whole genome sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mlst", + "Galaxy tool ids": [ + "mlst", + "mlst_list" + ], + "Description": "Scan contig files against PubMLST typing schemes", + "bio.tool id": "mlst", + "bio.tool ids": [ + "mlst" + ], + "biii": null, + "bio.tool name": "MLST", + "bio.tool description": "Multi Locus Sequence Typing from an assembled genome or from a set of reads.", + "EDAM operation": [ + "Multilocus sequence typing" + ], + "EDAM topic": [ + "Immunoproteins and antigens" + ], + "Status": "To update", + "Source": "https://github.com/tseemann/mlst", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mlst", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst", + "Galaxy wrapper version": "2.22.0", + "Conda id": "mlst", + "Conda version": "2.23.0", + "EDAM operation (no superclasses)": [ + "Multilocus sequence typing" + ], + "EDAM topic (no superclasses)": [ + "Immunoproteins and antigens" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "moabs", + "Galaxy tool ids": [ + "moabs" + ], + "Description": "MOABS for differential methylation analysis on Bisulfite sequencing data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/sunnyisgalaxy/moabs", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "moabs", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/sunnyisgalaxy/moabs", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs", + "Galaxy wrapper version": "1.3.4.6", + "Conda id": "moabs", + "Conda version": "1.3.9.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mosdepth", + "Galaxy tool ids": [ + "mosdepth" + ], + "Description": "fast and flexible BAM/CRAM depth calculation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/brentp/mosdepth", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "mosdepth", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth", + "Galaxy wrapper version": "0.3.8", + "Conda id": "mosdepth", + "Conda version": "0.3.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mothur", + "Galaxy tool ids": [ + "mothur_align_check", + "mothur_align_seqs", + "mothur_amova", + "mothur_anosim", + "mothur_bin_seqs", + "mothur_biom_info", + "mothur_chimera_bellerophon", + "mothur_chimera_ccode", + "mothur_chimera_check", + "mothur_chimera_perseus", + "mothur_chimera_pintail", + "mothur_chimera_slayer", + "mothur_chimera_uchime", + "mothur_chimera_vsearch", + "mothur_chop_seqs", + "mothur_classify_otu", + "mothur_classify_seqs", + "mothur_classify_tree", + "mothur_clearcut", + "mothur_cluster_classic", + "mothur_cluster_fragments", + "mothur_cluster_split", + "mothur_cluster", + "mothur_collect_shared", + "mothur_collect_single", + "mothur_consensus_seqs", + "mothur_cooccurrence", + "mothur_corr_axes", + "mothur_count_groups", + "mothur_count_seqs", + "mothur_create_database", + "mothur_degap_seqs", + "mothur_deunique_seqs", + "mothur_deunique_tree", + "mothur_dist_seqs", + "mothur_dist_shared", + "mothur_fastq_info", + "mothur_filter_seqs", + "mothur_filter_shared", + "mothur_get_communitytype", + "mothur_get_coremicrobiome", + "mothur_get_dists", + "mothur_get_group", + "mothur_get_groups", + "mothur_get_label", + "mothur_get_lineage", + "mothur_get_mimarkspackage", + "mothur_get_otulabels", + "mothur_get_otulist", + "mothur_get_oturep", + "mothur_get_otus", + "mothur_get_rabund", + "mothur_get_relabund", + "mothur_get_sabund", + "mothur_get_seqs", + "mothur_get_sharedseqs", + "mothur_heatmap_bin", + "mothur_heatmap_sim", + "mothur_homova", + "mothur_indicator", + "mothur_lefse", + "mothur_libshuff", + "mothur_list_otulabels", + "mothur_list_seqs", + "mothur_make_biom", + "mothur_make_contigs", + "mothur_make_design", + "mothur_make_fastq", + "mothur_make_group", + "mothur_make_lefse", + "mothur_make_lookup", + "mothur_make_shared", + "mothur_make_sra", + "mothur_mantel", + "mothur_merge_count", + "mothur_merge_files", + "mothur_merge_groups", + "mothur_merge_sfffiles", + "mothur_merge_taxsummary", + "mothur_metastats", + "mothur_mimarks_attributes", + "mothur_nmds", + "mothur_normalize_shared", + "mothur_otu_association", + "mothur_otu_hierarchy", + "mothur_pairwise_seqs", + "mothur_parse_list", + "mothur_parsimony", + "mothur_pca", + "mothur_pcoa", + "mothur_pcr_seqs", + "mothur_phylo_diversity", + "mothur_phylotype", + "mothur_pre_cluster", + "mothur_primer_design", + "mothur_rarefaction_shared", + "mothur_rarefaction_single", + "mothur_remove_dists", + "mothur_remove_groups", + "mothur_remove_lineage", + "mothur_remove_otulabels", + "mothur_remove_otus", + "mothur_remove_rare", + "mothur_remove_seqs", + "mothur_rename_seqs", + "mothur_reverse_seqs", + "mothur_screen_seqs", + "mothur_sens_spec", + "mothur_seq_error", + "mothur_sffinfo", + "mothur_shhh_flows", + "mothur_shhh_seqs", + "mothur_sort_seqs", + "mothur_split_abund", + "mothur_split_groups", + "mothur_sub_sample", + "mothur_summary_qual", + "mothur_summary_seqs", + "mothur_summary_shared", + "mothur_summary_single", + "mothur_summary_tax", + "mothur_taxonomy_to_krona", + "mothur_tree_shared", + "mothur_trim_flows", + "mothur_trim_seqs", + "mothur_unifrac_unweighted", + "mothur_unifrac_weighted", + "mothur_unique_seqs", + "mothur_venn" + ], + "Description": "Mothur wrappers", + "bio.tool id": "mothur", + "bio.tool ids": [ + "mothur" + ], + "biii": null, + "bio.tool name": "mothur", + "bio.tool description": "Open-source, platform-independent, community-supported software for describing and comparing microbial communities", + "EDAM operation": [ + "DNA barcoding", + "Sequencing quality control", + "Sequence clustering", + "Taxonomic classification", + "Visualisation", + "Sequence read processing", + "Phylogenetic analysis" + ], + "EDAM topic": [ + "Microbial ecology", + "Taxonomy", + "Sequence analysis", + "Phylogeny" + ], + "Status": "To update", + "Source": "https://www.mothur.org", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "mothur", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur", + "Galaxy wrapper version": "1.0", + "Conda id": "mothur", + "Conda version": "1.48.0", + "EDAM operation (no superclasses)": [ + "DNA barcoding", + "Sequencing quality control", + "Sequence clustering", + "Taxonomic classification", + "Visualisation", + "Sequence read processing", + "Phylogenetic analysis" + ], + "EDAM topic (no superclasses)": [ + "Microbial ecology", + "Taxonomy", + "Sequence analysis", + "Phylogeny" + ], + "Available on UseGalaxy.org": 129, + "Available on UseGalaxy.org.au": 129, + "Available on UseGalaxy.eu": 129, + "Available on UseGalaxy.org.fr": 129 + }, + { + "Galaxy wrapper id": "msaboot", + "Galaxy tool ids": [ + "msaboot" + ], + "Description": "A multiple sequences alignment bootstrapping tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/phac-nml/msaboot", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "msaboot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot", + "Galaxy wrapper version": "0.1.2", + "Conda id": "msaboot", + "Conda version": "0.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "multigps", + "Galaxy tool ids": [ + "multigps" + ], + "Description": "Analyzes collections of multi-condition ChIP-seq data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://mahonylab.org/software/multigps/", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "multigps", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps", + "Galaxy wrapper version": "0.74.0", + "Conda id": "fonts-conda-ecosystem", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "multigsea", + "Galaxy tool ids": [ + "multigsea" + ], + "Description": "GSEA-based pathway enrichment analysis for multi-omics data", + "bio.tool id": "multiGSEA", + "bio.tool ids": [ + "multiGSEA" + ], + "biii": null, + "bio.tool name": "multiGSEA", + "bio.tool description": "A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.", + "EDAM operation": [ + "Gene-set enrichment analysis", + "Aggregation", + "Pathway analysis" + ], + "EDAM topic": [ + "Metabolomics", + "Molecular interactions, pathways and networks", + "Proteomics", + "Transcriptomics", + "Small molecules" + ], + "Status": "Up-to-date", + "Source": "https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html", + "ToolShed categories": [ + "Transcriptomics", + "Proteomics", + "Statistics" + ], + "ToolShed id": "multigsea", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea", + "Galaxy wrapper version": "1.12.0", + "Conda id": "bioconductor-multigsea", + "Conda version": "1.12.0", + "EDAM operation (no superclasses)": [ + "Gene-set enrichment analysis", + "Aggregation", + "Pathway analysis" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics", + "Molecular interactions, pathways and networks", + "Proteomics", + "Transcriptomics", + "Small molecules" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "multiqc", + "Galaxy tool ids": [ + "multiqc" + ], + "Description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report", + "bio.tool id": "multiqc", + "bio.tool ids": [ + "multiqc" + ], + "biii": null, + "bio.tool name": "MultiQC", + "bio.tool description": "MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.", + "EDAM operation": [ + "Validation", + "Sequencing quality control" + ], + "EDAM topic": [ + "Sequencing", + "Bioinformatics", + "Sequence analysis", + "Genomics" + ], + "Status": "To update", + "Source": "http://multiqc.info/", + "ToolShed categories": [ + "Fastq Manipulation", + "Statistics", + "Visualization" + ], + "ToolShed id": "multiqc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc", + "Galaxy wrapper version": "1.11", + "Conda id": "multiqc", + "Conda version": "1.22.2", + "EDAM operation (no superclasses)": [ + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Bioinformatics", + "Sequence analysis", + "Genomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "mummer4", + "Galaxy tool ids": [ + "mummer_delta_filter", + "mummer_dnadiff", + "mummer_mummer", + "mummer_mummerplot", + "mummer_nucmer", + "mummer_show_coords" + ], + "Description": "Mummer4 Tools", + "bio.tool id": "mummer4", + "bio.tool ids": [ + "mummer4" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/mummer4/mummer", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mummer4", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4", + "Galaxy wrapper version": "4.0.0rc1", + "Conda id": "mummer4", + "Conda version": "4.0.0rc1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 6, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 6 + }, + { + "Galaxy wrapper id": "mykrobe", + "Galaxy tool ids": [ + "mykrobe_predict" + ], + "Description": "Antibiotic resistance predictions", + "bio.tool id": "Mykrobe", + "bio.tool ids": [ + "Mykrobe" + ], + "biii": null, + "bio.tool name": "Mykrobe", + "bio.tool description": "Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed", + "EDAM operation": [ + "Antimicrobial resistance prediction", + "Variant calling", + "Genotyping", + "Sequence trimming" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Genotype and phenotype", + "Probes and primers", + "Genetic variation", + "Metagenomics" + ], + "Status": "To update", + "Source": "https://github.com/Mykrobe-tools/mykrobe", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "mykrobe", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe", + "Galaxy wrapper version": "0.10.0", + "Conda id": "mykrobe", + "Conda version": "0.13.0", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction", + "Variant calling", + "Genotyping", + "Sequence trimming" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Genotype and phenotype", + "Probes and primers", + "Genetic variation", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mzmine", + "Galaxy tool ids": [ + "mzmine_batch" + ], + "Description": "mass-spectrometry data processing, with the main focus on LC-MS data", + "bio.tool id": "mzmine", + "bio.tool ids": [ + "mzmine" + ], + "biii": null, + "bio.tool name": "MZmine", + "bio.tool description": "Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.", + "EDAM operation": [ + "Natural product identification", + "Standardisation and normalisation", + "Peptide database search", + "Deisotoping", + "Clustering", + "Filtering", + "Chromatographic alignment", + "Peak detection", + "Peptide identification", + "Chromatogram visualisation", + "Mass spectrum visualisation", + "Structure visualisation", + "Plotting", + "Heat map generation" + ], + "EDAM topic": [ + "Proteomics", + "Metabolomics", + "Proteomics experiment", + "Small molecules" + ], + "Status": "Up-to-date", + "Source": "http://mzmine.github.io/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "mzmine_batch", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine", + "Galaxy wrapper version": "3.9.0", + "Conda id": "mzmine", + "Conda version": "3.9.0", + "EDAM operation (no superclasses)": [ + "Natural product identification", + "Standardisation and normalisation", + "Peptide database search", + "Deisotoping", + "Clustering", + "Filtering", + "Chromatographic alignment", + "Peak detection", + "Peptide identification", + "Chromatogram visualisation", + "Mass spectrum visualisation", + "Structure visualisation", + "Plotting", + "Heat map generation" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Metabolomics", + "Proteomics experiment", + "Small molecules" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "naltorfs", + "Galaxy tool ids": [ + "bicodon_counts_from_fasta", + "codon_freq_from_bicodons", + "find_nested_alt_orfs" + ], + "Description": "nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/BlankenbergLab/nAltORFs", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs", + "Galaxy wrapper version": "0.1.2", + "Conda id": "naltorfs", + "Conda version": "0.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "nanocompore", + "Galaxy tool ids": [ + "nanocompore_db", + "nanocompore_sampcomp" + ], + "Description": "Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.", + "bio.tool id": "Nanocompore", + "bio.tool ids": [ + "Nanocompore" + ], + "biii": null, + "bio.tool name": "Nanocompore", + "bio.tool description": "RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro", + "EDAM operation": [ + "Post-translation modification site prediction", + "PolyA signal detection", + "Genotyping", + "k-mer counting" + ], + "EDAM topic": [ + "Functional, regulatory and non-coding RNA", + "RNA-Seq", + "Gene transcripts", + "Transcriptomics", + "Transcription factors and regulatory sites" + ], + "Status": "To update", + "Source": "https://nanocompore.rna.rocks/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "nanocompore", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore", + "Galaxy wrapper version": "1.0.0rc3.post2", + "Conda id": "nanocompore", + "Conda version": "1.0.4", + "EDAM operation (no superclasses)": [ + "PolyA signal detection", + "Genotyping", + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Functional, regulatory and non-coding RNA", + "RNA-Seq", + "Gene transcripts", + "Transcriptomics", + "Transcription factors and regulatory sites" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "nanoplot", + "Galaxy tool ids": [ + "nanoplot" + ], + "Description": "Plotting tool for long read sequencing data and alignments", + "bio.tool id": "nanoplot", + "bio.tool ids": [ + "nanoplot" + ], + "biii": null, + "bio.tool name": "NanoPlot", + "bio.tool description": "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences", + "EDAM operation": [ + "Scatter plot plotting", + "Box-Whisker plot plotting" + ], + "EDAM topic": [ + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/wdecoster/NanoPlot", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "nanoplot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot", + "Galaxy wrapper version": "1.42.0", + "Conda id": "nanoplot", + "Conda version": "1.42.0", + "EDAM operation (no superclasses)": [ + "Scatter plot plotting", + "Box-Whisker plot plotting" + ], + "EDAM topic (no superclasses)": [ + "Genomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "nanopolishcomp", + "Galaxy tool ids": [ + "nanopolishcomp_eventaligncollapse", + "nanopolishcomp_freqmethcalculate" + ], + "Description": "NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.", + "bio.tool id": "nanopolishcomp", + "bio.tool ids": [ + "nanopolishcomp" + ], + "biii": null, + "bio.tool name": "NanopolishComp", + "bio.tool description": "NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.", + "EDAM operation": [ + "Methylation analysis", + "Collapsing methods" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequencing", + "Genetic variation" + ], + "Status": "To update", + "Source": "https://a-slide.github.io/NanopolishComp", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "nanopolishcomp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp", + "Galaxy wrapper version": "0.6.11", + "Conda id": "nanopolishcomp", + "Conda version": "0.6.12", + "EDAM operation (no superclasses)": [ + "Methylation analysis", + "Collapsing methods" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Sequencing", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "ncbi_acc_download", + "Galaxy tool ids": [ + "ncbi_acc_download" + ], + "Description": "Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/kblin/ncbi-acc-download", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "ncbi_acc_download", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download", + "Galaxy wrapper version": "0.2.8", + "Conda id": "ncbi-acc-download", + "Conda version": "0.2.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ncbi_datasets", + "Galaxy tool ids": [ + "datasets_download_gene", + "datasets_download_genome" + ], + "Description": "NCBI datasets downloads biological sequence data across all domains of life from NCBI.", + "bio.tool id": "ncbi_datasets", + "bio.tool ids": [ + "ncbi_datasets" + ], + "biii": null, + "bio.tool name": "NCBI Datasets", + "bio.tool description": "NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.", + "EDAM operation": [ + "Data handling", + "Sequence database search", + "Data retrieval" + ], + "EDAM topic": [ + "Biological databases" + ], + "Status": "To update", + "Source": "https://github.com/ncbi/datasets", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "ncbi_datasets", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets", + "Galaxy wrapper version": "16.6.0", + "Conda id": "ncbi-datasets-cli", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Data handling", + "Sequence database search", + "Data retrieval" + ], + "EDAM topic (no superclasses)": [ + "Biological databases" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "ncbi_entrez_direct", + "Galaxy tool ids": [ + "ncbi_entrez_direct_efetch", + "ncbi_entrez_direct_einfo", + "ncbi_entrez_direct_esearch" + ], + "Description": "NCBI Entrez Direct allow fetching data from NCBI Databases", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://www.ncbi.nlm.nih.gov/books/NBK179288/", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "ncbi_entrez_direct", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct", + "Galaxy wrapper version": "21.6", + "Conda id": "entrez-direct", + "Conda version": "21.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ncbi_entrez_eutils", + "Galaxy tool ids": [ + "ncbi_eutils_ecitmatch", + "ncbi_eutils_efetch", + "ncbi_eutils_egquery", + "ncbi_eutils_einfo", + "ncbi_eutils_elink", + "ncbi_eutils_epost", + "ncbi_eutils_esearch", + "ncbi_eutils_esummary" + ], + "Description": "NCBI Entrez E-Utilties allow fetching data from NCBI Databases", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ncbi.nlm.nih.gov/books/NBK25501/", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "ncbi_entrez_eutils", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils", + "Galaxy wrapper version": "1.70", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ncbi_fcs_gx", + "Galaxy tool ids": [ + "ncbi_fcs_gx" + ], + "Description": "FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).", + "bio.tool id": "ncbi_fcs", + "bio.tool ids": [ + "ncbi_fcs" + ], + "biii": null, + "bio.tool name": "NCBI fcs", + "bio.tool description": "The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.", + "EDAM operation": [ + "Sequence assembly validation", + "Sequence trimming", + "Sequence contamination filtering" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ncbi/fcs-gx", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ncbi_fcs_gx", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx", + "Galaxy wrapper version": "0.5.0", + "Conda id": "ncbi-fcs-gx", + "Conda version": "0.5.0", + "EDAM operation (no superclasses)": [ + "Sequence assembly validation", + "Sequence trimming", + "Sequence contamination filtering" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "necat", + "Galaxy tool ids": [ + "necat" + ], + "Description": "Error correction and de-novo assembly for ONT Nanopore reads", + "bio.tool id": "necat", + "bio.tool ids": [ + "necat" + ], + "biii": null, + "bio.tool name": "NECAT", + "bio.tool description": "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.", + "EDAM operation": [ + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/xiaochuanle/NECAT", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "necat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat", + "Galaxy wrapper version": "0.0.1_update20200803", + "Conda id": "necat", + "Conda version": "0.0.1_update20200803", + "EDAM operation (no superclasses)": [ + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "newick_utils", + "Galaxy tool ids": [ + "newick_display" + ], + "Description": "Perform operations on Newick trees", + "bio.tool id": "newick_utilities", + "bio.tool ids": [ + "newick_utilities" + ], + "biii": null, + "bio.tool name": "Newick Utilities", + "bio.tool description": "The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.", + "EDAM operation": [ + "Phylogenetic tree generation", + "Phylogenetic tree analysis", + "Phylogenetic tree reconstruction" + ], + "EDAM topic": [ + "Phylogeny", + "Genomics", + "Computer science" + ], + "Status": "To update", + "Source": "http://cegg.unige.ch/newick_utils", + "ToolShed categories": [ + "Visualization", + "Metagenomics" + ], + "ToolShed id": "newick_utils", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/tjunier/newick_utils", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils", + "Galaxy wrapper version": "1.6+galaxy1", + "Conda id": "newick_utils", + "Conda version": "1.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Phylogeny", + "Genomics", + "Computer science" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "nextclade", + "Galaxy tool ids": [ + "nextalign", + "nextclade" + ], + "Description": "Identify differences between your sequences and a reference sequence used by Nextstrain", + "bio.tool id": "nextclade", + "bio.tool ids": [ + "nextclade" + ], + "biii": null, + "bio.tool name": "Nextclade", + "bio.tool description": "Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.", + "EDAM operation": [ + "Methylation analysis", + "Variant calling" + ], + "EDAM topic": [ + "Genomics", + "Sequence analysis", + "Cladistics" + ], + "Status": "To update", + "Source": "https://github.com/nextstrain/nextclade", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade", + "Galaxy wrapper version": "2.7.0", + "Conda id": "nextalign", + "Conda version": "2.14.0", + "EDAM operation (no superclasses)": [ + "Methylation analysis", + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Cladistics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "ngmlr", + "Galaxy tool ids": [ + "ngmlr" + ], + "Description": "CoNvex Gap-cost alignMents for Long Reads", + "bio.tool id": "ngmlr", + "bio.tool ids": [ + "ngmlr" + ], + "biii": null, + "bio.tool name": "NGMLR", + "bio.tool description": "An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.", + "EDAM operation": [ + "DNA mapping", + "Sequence alignment", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Sequencing", + "Mapping", + "DNA structural variation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/philres/ngmlr", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "ngmlr", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr", + "Galaxy wrapper version": "0.2.7", + "Conda id": "ngmlr", + "Conda version": "0.2.7", + "EDAM operation (no superclasses)": [ + "DNA mapping", + "Sequence alignment", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ngsutils", + "Galaxy tool ids": [ + "ngsutils_bam_filter" + ], + "Description": "NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.", + "bio.tool id": "ngsutils", + "bio.tool ids": [ + "ngsutils" + ], + "biii": null, + "bio.tool name": "NGSUtils", + "bio.tool description": "NGSUtils is a suite of software tools for working with next-generation sequencing datasets", + "EDAM operation": [ + "Read pre-processing", + "Sequencing quality control", + "Variant calling", + "Formatting", + "Sequence contamination filtering" + ], + "EDAM topic": [ + "Genomics", + "Transcriptomics" + ], + "Status": "To update", + "Source": "https://github.com/ngsutils/ngsutils", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils", + "Galaxy wrapper version": null, + "Conda id": "ngsutils", + "Conda version": "0.5.9", + "EDAM operation (no superclasses)": [ + "Read pre-processing", + "Variant calling", + "Formatting", + "Sequence contamination filtering" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "nonpareil", + "Galaxy tool ids": [ + "nonpareil" + ], + "Description": "Estimate average coverage in metagenomic datasets", + "bio.tool id": "nonpareil", + "bio.tool ids": [ + "nonpareil" + ], + "biii": null, + "bio.tool name": "nonpareil", + "bio.tool description": "Estimate metagenomic coverage and sequence diversity", + "EDAM operation": [ + "Operation" + ], + "EDAM topic": [], + "Status": "To update", + "Source": "http://nonpareil.readthedocs.io", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "nonpareil", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil", + "Galaxy wrapper version": "3.1.1", + "Conda id": "nonpareil", + "Conda version": "3.4.1", + "EDAM operation (no superclasses)": [ + "Operation" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "novoplasty", + "Galaxy tool ids": [ + "novoplasty" + ], + "Description": "NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ndierckx/NOVOPlasty", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "novoplasty", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty", + "Galaxy wrapper version": "4.3.1", + "Conda id": "novoplasty", + "Conda version": "4.3.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "nugen_nudup", + "Galaxy tool ids": [ + "nugen_nudup" + ], + "Description": "Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.", + "bio.tool id": "nudup", + "bio.tool ids": [ + "nudup" + ], + "biii": null, + "bio.tool name": "NuDup", + "bio.tool description": "Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.", + "EDAM operation": [ + "Duplication detection" + ], + "EDAM topic": [ + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tecangenomics/nudup", + "ToolShed categories": [ + "SAM", + "Metagenomics", + "Sequence Analysis", + "Transcriptomics" + ], + "ToolShed id": "nugen_nudup", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup", + "Galaxy wrapper version": "2.3.3", + "Conda id": "nudup", + "Conda version": "2.3.3", + "EDAM operation (no superclasses)": [ + "Duplication detection" + ], + "EDAM topic (no superclasses)": [ + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "obitools", + "Galaxy tool ids": [ + "obi_illumina_pairend", + "obi_ngsfilter", + "obi_annotate", + "obi_clean", + "obi_convert", + "obi_grep", + "obi_sort", + "obi_stat", + "obi_tab", + "obi_uniq" + ], + "Description": "OBITools is a set of programs developed to simplify the manipulation of sequence files", + "bio.tool id": "obitools", + "bio.tool ids": [ + "obitools" + ], + "biii": null, + "bio.tool name": "OBITools", + "bio.tool description": "Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.", + "EDAM operation": [ + "Sequence analysis", + "Sequence analysis" + ], + "EDAM topic": [ + "Sequence analysis", + "DNA", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "http://metabarcoding.org/obitools", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "obitools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools", + "Galaxy wrapper version": "1.2.13", + "Conda id": "obitools", + "Conda version": "1.2.13", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "DNA", + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 10, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.org.fr": 10 + }, + { + "Galaxy wrapper id": "ococo", + "Galaxy tool ids": [ + "ococo" + ], + "Description": "Variant detection of SNVs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/karel-brinda/ococo", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "ococo", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo", + "Galaxy wrapper version": "0.1.2.6", + "Conda id": "ococo", + "Conda version": "0.1.2.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "odgi", + "Galaxy tool ids": [ + "odgi_build", + "odgi_viz" + ], + "Description": "Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/vgteam/odgi", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi", + "Galaxy wrapper version": "0.3", + "Conda id": "odgi", + "Conda version": "0.8.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "omark", + "Galaxy tool ids": [ + "omark" + ], + "Description": "Proteome quality assessment software", + "bio.tool id": "omark", + "bio.tool ids": [ + "omark" + ], + "biii": null, + "bio.tool name": "OMArk", + "bio.tool description": "Proteome quality assessment software", + "EDAM operation": [ + "Sequence assembly validation", + "Differential protein expression profiling" + ], + "EDAM topic": [ + "Proteomics", + "Sequence analysis", + "Statistics and probability" + ], + "Status": "To update", + "Source": "https://github.com/DessimozLab/OMArk", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "omark", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark", + "Galaxy wrapper version": "0.3.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Sequence assembly validation", + "Differential protein expression profiling" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Sequence analysis", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ont_fast5_api", + "Galaxy tool ids": [ + "ont_fast5_api_compress_fast5", + "ont_fast5_api_fast5_subset", + "ont_fast5_api_multi_to_single_fast5", + "ont_fast5_api_single_to_multi_fast5" + ], + "Description": "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nanoporetech/ont_fast5_api/", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "ont_fast5_api", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api", + "Galaxy wrapper version": "3.1.3", + "Conda id": "ont-fast5-api", + "Conda version": "4.1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "onto_toolkit", + "Galaxy tool ids": [ + "onto_tk_get_ancestor_terms", + "onto_tk_get_child_terms", + "onto_tk_get_descendent_terms", + "onto_tk_get_parent_terms", + "onto_tk_get_parent_terms_by_relationship_type", + "onto_tk_get_relationship_id_vs_relationship_def", + "onto_tk_get_relationship_id_vs_relationship_name", + "onto_tk_get_relationship_id_vs_relationship_namespace", + "onto_tk_get_relationship_types", + "onto_tk_get_root_terms", + "onto_tk_get_subontology_from", + "onto_tk_term_id_vs_term_def", + "onto_tk_term_id_vs_term_name", + "onto_tk_get_term_synonyms", + "onto_tk_get_terms", + "onto_tk_get_terms_by_relationship_type", + "onto_tk_obo2owl", + "onto_tk_obo2rdf", + "onto_tk_term_id_vs_term_def" + ], + "Description": "ONTO-Toolkit is a collection of tools for managing ontologies.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://search.cpan.org/~easr/ONTO-PERL-1.45/", + "ToolShed categories": [ + "Ontology Manipulation" + ], + "ToolShed id": "onto_toolkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit", + "Galaxy wrapper version": "1.45", + "Conda id": "perl-onto-perl", + "Conda version": "1.45", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 17, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "optdoe", + "Galaxy tool ids": [ + "optdoe" + ], + "Description": "Optimal Design Of Experiment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/pablocarb/doebase", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "optdoe", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe", + "Galaxy wrapper version": "v2.0.2", + "Conda id": "doebase", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "optitype", + "Galaxy tool ids": [ + "optitype" + ], + "Description": "Precision HLA typing from NGS data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/FRED-2/OptiType", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "optitype", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype", + "Galaxy wrapper version": "1.3.5", + "Conda id": "optitype", + "Conda version": "1.3.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "orfipy", + "Galaxy tool ids": [ + "orfipy" + ], + "Description": "Galaxy wrapper for ORFIPY", + "bio.tool id": "orfipy", + "bio.tool ids": [ + "orfipy" + ], + "biii": null, + "bio.tool name": "orfipy", + "bio.tool description": "A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.", + "EDAM operation": [ + "Coding region prediction", + "Database search", + "Transcriptome assembly", + "De-novo assembly" + ], + "EDAM topic": [ + "Computer science", + "RNA-Seq", + "Transcriptomics", + "Small molecules" + ], + "Status": "Up-to-date", + "Source": "https://github.com/urmi-21/orfipy", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "orfipy", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy", + "Galaxy wrapper version": "0.0.4", + "Conda id": "orfipy", + "Conda version": "0.0.4", + "EDAM operation (no superclasses)": [ + "Coding region prediction", + "Database search", + "Transcriptome assembly", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Computer science", + "RNA-Seq", + "Transcriptomics", + "Small molecules" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "orthofinder", + "Galaxy tool ids": [ + "orthofinder_onlygroups" + ], + "Description": "Accurate inference of orthologous gene groups made easy", + "bio.tool id": "OrthoFinder", + "bio.tool ids": [ + "OrthoFinder" + ], + "biii": null, + "bio.tool name": "OrthoFinder", + "bio.tool description": "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.", + "EDAM operation": [ + "Genome comparison", + "Phylogenetic tree generation (from molecular sequences)", + "Phylogenetic tree analysis", + "Genome alignment" + ], + "EDAM topic": [ + "Phylogenetics", + "Phylogenomics", + "Bioinformatics", + "Comparative genomics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/davidemms/OrthoFinder", + "ToolShed categories": [ + "Phylogenetics", + "Sequence Analysis" + ], + "ToolShed id": "orthofinder", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder", + "Galaxy wrapper version": "2.5.5", + "Conda id": "orthofinder", + "Conda version": "2.5.5", + "EDAM operation (no superclasses)": [ + "Genome comparison", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics", + "Phylogenomics", + "Bioinformatics", + "Comparative genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "packaged_annotation_loader", + "Galaxy tool ids": [ + "packaged_annotation_loader" + ], + "Description": "Tool to make cached genome annotation data available as a list of datasets collection", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "packaged_annotation_loader", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader", + "Galaxy wrapper version": "0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pairtools", + "Galaxy tool ids": [ + "pairtools_dedup", + "pairtools_parse", + "pairtools_sort", + "pairtools_split", + "pairtools_stats" + ], + "Description": "Flexible tools for Hi-C data processing", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://pairtools.readthedocs.io", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pairtools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/open2c/pairtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools", + "Galaxy wrapper version": "1.1.0", + "Conda id": "pairtools", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pangolin", + "Galaxy tool ids": [ + "pangolin" + ], + "Description": "Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.", + "bio.tool id": "pangolin_cov-lineages", + "bio.tool ids": [ + "pangolin_cov-lineages" + ], + "biii": null, + "bio.tool name": "pangolin", + "bio.tool description": "Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages", + "EDAM operation": [ + "Tree-based sequence alignment", + "Variant classification" + ], + "EDAM topic": [ + "Virology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/cov-lineages/pangolin", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pangolin", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin", + "Galaxy wrapper version": "4.3", + "Conda id": "pangolin", + "Conda version": "4.3", + "EDAM operation (no superclasses)": [ + "Tree-based sequence alignment", + "Variant classification" + ], + "EDAM topic (no superclasses)": [ + "Virology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "parse_mito_blast", + "Galaxy tool ids": [ + "parse_mito_blast" + ], + "Description": "Filtering blast out from querying assembly against mitochondrial database.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "parse_mito_blast", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast", + "Galaxy wrapper version": "1.0.2", + "Conda id": "parse_mito_blast", + "Conda version": "1.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pathview", + "Galaxy tool ids": [ + "pathview" + ], + "Description": "Pathview is a tool set for pathway based data integration and visualization.", + "bio.tool id": "pathview", + "bio.tool ids": [ + "pathview" + ], + "biii": null, + "bio.tool name": "pathview", + "bio.tool description": "Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.", + "EDAM operation": [ + "Pathway or network analysis", + "Pathway or network visualisation" + ], + "EDAM topic": [ + "Molecular interactions, pathways and networks", + "Systems biology", + "Data visualisation" + ], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/pathview.html", + "ToolShed categories": [ + "Statistics", + "RNA", + "Micro-array Analysis" + ], + "ToolShed id": "pathview", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview", + "Galaxy wrapper version": "1.34.0", + "Conda id": "bioconductor-pathview", + "Conda version": "1.42.0", + "EDAM operation (no superclasses)": [ + "Pathway or network analysis", + "Pathway or network visualisation" + ], + "EDAM topic (no superclasses)": [ + "Molecular interactions, pathways and networks", + "Systems biology", + "Data visualisation" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "pbgcpp", + "Galaxy tool ids": [ + "pbgcpp" + ], + "Description": "Compute genomic consensus and call variants using PacBio reads mapped to a reference", + "bio.tool id": "genomicconsensus", + "bio.tool ids": [ + "genomicconsensus" + ], + "biii": null, + "bio.tool name": "GenomicConsensus", + "bio.tool description": "The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.", + "EDAM operation": [ + "Variant calling" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/PacificBiosciences/gcpp", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pbgcpp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp", + "Galaxy wrapper version": "2.0.2", + "Conda id": "pbgcpp", + "Conda version": "2.0.2", + "EDAM operation (no superclasses)": [ + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pbmm2", + "Galaxy tool ids": [ + "pbmm2" + ], + "Description": "A minimap2 SMRT wrapper for PacBio data.", + "bio.tool id": "pbmm2", + "bio.tool ids": [ + "pbmm2" + ], + "biii": null, + "bio.tool name": "pbmm2", + "bio.tool description": "pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.", + "EDAM operation": [ + "Pairwise sequence alignment", + "Sorting" + ], + "EDAM topic": [ + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/PacificBiosciences/pbmm2", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "pbmm2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2", + "Galaxy wrapper version": "1.13.1", + "Conda id": "pbmm2", + "Conda version": "1.13.1", + "EDAM operation (no superclasses)": [ + "Pairwise sequence alignment", + "Sorting" + ], + "EDAM topic (no superclasses)": [ + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pbtk", + "Galaxy tool ids": [ + "bam2fastx" + ], + "Description": "Convert PacBio Bam File to fasta or fastq file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/PacificBiosciences/pbtk", + "ToolShed categories": [ + "Convert Formats", + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "bam2fastx", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk", + "Galaxy wrapper version": "3.1.1", + "Conda id": "pbtk", + "Conda version": "3.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pe_histogram", + "Galaxy tool ids": [ + "pe_histogram" + ], + "Description": "Contains a tool that produces an insert size histogram for a paired-end BAM file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram", + "ToolShed categories": [ + "Graphics" + ], + "ToolShed id": "pe_histogram", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram", + "Galaxy wrapper version": "1.0.1", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "peakzilla", + "Galaxy tool ids": [ + "peakzilla" + ], + "Description": "Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/steinmann/peakzilla", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "peakzilla", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla", + "Galaxy wrapper version": "1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pear", + "Galaxy tool ids": [ + "iuc_pear" + ], + "Description": "PEAR evaluates all possible paired-end read overlaps", + "bio.tool id": "pear", + "bio.tool ids": [ + "pear" + ], + "biii": null, + "bio.tool name": "PEAR", + "bio.tool description": "Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.", + "EDAM operation": [ + "Sequence merging" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "pear", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear", + "Galaxy wrapper version": "0.9.6", + "Conda id": "pear", + "Conda version": "0.9.6", + "EDAM operation (no superclasses)": [ + "Sequence merging" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pharokka", + "Galaxy tool ids": [ + "pharokka" + ], + "Description": "rapid standardised annotation tool for bacteriophage genomes and metagenomes", + "bio.tool id": "pharokka", + "bio.tool ids": [ + "pharokka" + ], + "biii": null, + "bio.tool name": "Pharokka", + "bio.tool description": "Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.", + "EDAM operation": [ + "Genome annotation", + "Antimicrobial resistance prediction", + "tRNA gene prediction", + "Formatting", + "Sequence assembly" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence sites, features and motifs", + "Workflows", + "Functional, regulatory and non-coding RNA" + ], + "Status": "To update", + "Source": "https://github.com/gbouras13/pharokka", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "pharokka", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka", + "Galaxy wrapper version": "1.3.2", + "Conda id": "\n pharokka\n ", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Genome annotation", + "Antimicrobial resistance prediction", + "tRNA gene prediction", + "Formatting", + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence sites, features and motifs", + "Workflows", + "Functional, regulatory and non-coding RNA" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "phyloseq", + "Galaxy tool ids": [ + "phyloseq_from_biom", + "phyloseq_from_dada2", + "phyloseq_plot_ordination", + "phyloseq_plot_richness" + ], + "Description": "Handling and analysis of high-throughput microbiome census data", + "bio.tool id": "phyloseq", + "bio.tool ids": [ + "phyloseq" + ], + "biii": null, + "bio.tool name": "phyloseq", + "bio.tool description": "Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.", + "EDAM operation": [ + "Deposition", + "Analysis", + "Visualisation" + ], + "EDAM topic": [ + "Microbiology", + "Sequence analysis", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "phyloseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq", + "Galaxy wrapper version": "1.46.0", + "Conda id": "bioconductor-phyloseq", + "Conda version": "1.46.0", + "EDAM operation (no superclasses)": [ + "Deposition", + "Analysis", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Sequence analysis", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "phyml", + "Galaxy tool ids": [ + "phyml" + ], + "Description": "PhyML is a phylogeny software based on the maximum-likelihood principle.", + "bio.tool id": "phyml", + "bio.tool ids": [ + "phyml" + ], + "biii": null, + "bio.tool name": "PhyML", + "bio.tool description": "Phylogenetic estimation software using Maximum Likelihood", + "EDAM operation": [ + "Phylogenetic tree generation (maximum likelihood and Bayesian methods)" + ], + "EDAM topic": [ + "Phylogenetics", + "Bioinformatics", + "Phylogenetics" + ], + "Status": "Up-to-date", + "Source": "http://www.atgc-montpellier.fr/phyml/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "phyml", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml", + "Galaxy wrapper version": "3.3.20220408", + "Conda id": "phyml", + "Conda version": "3.3.20220408", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Phylogenetics", + "Bioinformatics", + "Phylogenetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "picard", + "Galaxy tool ids": [ + "picard_AddCommentsToBam", + "picard_AddOrReplaceReadGroups", + "picard_BedToIntervalList", + "picard_CleanSam", + "picard_CASM", + "picard_CollectBaseDistributionByCycle", + "picard_CollectGcBiasMetrics", + "picard_CollectHsMetrics", + "picard_CollectInsertSizeMetrics", + "picard_CollectRnaSeqMetrics", + "picard_artifact_metrics", + "picard_CollectWgsMetrics", + "picard_DownsampleSam", + "picard_EstimateLibraryComplexity", + "picard_FastqToSam", + "picard_FilterSamReads", + "picard_FixMateInformation", + "picard_MarkDuplicates", + "picard_MarkDuplicatesWithMateCigar", + "picard_MeanQualityByCycle", + "picard_MergeBamAlignment", + "picard_MergeSamFiles", + "picard_NormalizeFasta", + "picard_QualityScoreDistribution", + "picard_ReorderSam", + "picard_ReplaceSamHeader", + "picard_RevertOriginalBaseQualitiesAndAddMateCigar", + "picard_RevertSam", + "picard_SamToFastq", + "picard_SortSam", + "picard_ValidateSamFile" + ], + "Description": "Picard SAM/BAM manipulation tools.", + "bio.tool id": "picard_samtofastq", + "bio.tool ids": [ + "picard_samtofastq", + "picard_fastqtosam", + "picard_reordersam", + "picard_replacesamheader" + ], + "biii": null, + "bio.tool name": "picard_samtofastq", + "bio.tool description": "Create a FASTQ file.", + "EDAM operation": [ + "Formatting" + ], + "EDAM topic": [ + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "http://broadinstitute.github.io/picard/", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "picard", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard", + "Galaxy wrapper version": "3.1.1", + "Conda id": "picard", + "Conda version": "3.1.1", + "EDAM operation (no superclasses)": [ + "Formatting" + ], + "EDAM topic (no superclasses)": [ + "Sequencing" + ], + "Available on UseGalaxy.org": 31, + "Available on UseGalaxy.org.au": 31, + "Available on UseGalaxy.eu": 31, + "Available on UseGalaxy.org.fr": 31 + }, + { + "Galaxy wrapper id": "pick_value", + "Galaxy tool ids": [ + "pick_value" + ], + "Description": "Compose a text parameter value using text, integer and float values", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "pick_value", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value", + "Galaxy wrapper version": "0.2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "picrust", + "Galaxy tool ids": [ + "picrust_categorize", + "picrust_compare_biom", + "picrust_format_tree_and_trait_table", + "picrust_metagenome_contributions", + "picrust_normalize_by_copy_number", + "picrust_predict_metagenomes" + ], + "Description": "PICRUSt wrappers", + "bio.tool id": "picrust", + "bio.tool ids": [ + "picrust" + ], + "biii": null, + "bio.tool name": "PICRUSt", + "bio.tool description": "PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.", + "EDAM operation": [ + "Phylogenetic reconstruction", + "Expression analysis", + "Genome annotation", + "DNA barcoding" + ], + "EDAM topic": [ + "Metagenomics", + "Microbial ecology", + "Functional, regulatory and non-coding RNA", + "Metagenomic sequencing" + ], + "Status": "To update", + "Source": "https://picrust.github.io/picrust/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "picrust", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust", + "Galaxy wrapper version": "1.1.1", + "Conda id": "picrust", + "Conda version": "1.1.4", + "EDAM operation (no superclasses)": [ + "Phylogenetic reconstruction", + "Expression analysis", + "Genome annotation", + "DNA barcoding" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbial ecology", + "Functional, regulatory and non-coding RNA", + "Metagenomic sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 6 + }, + { + "Galaxy wrapper id": "picrust2", + "Galaxy tool ids": [ + "picrust2_add_descriptions", + "picrust2_hsp", + "picrust2_metagenome_pipeline", + "picrust2_pathway_pipeline", + "picrust2_pipeline", + "picrust2_place_seqs", + "picrust2_shuffle_predictions" + ], + "Description": "PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States", + "bio.tool id": "picrust2", + "bio.tool ids": [ + "picrust2" + ], + "biii": null, + "bio.tool name": "PICRUSt2", + "bio.tool description": "PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.", + "EDAM operation": [ + "Phylogenetic reconstruction", + "Expression analysis", + "Rarefaction", + "Pathway analysis" + ], + "EDAM topic": [ + "Metagenomics", + "Microbiology", + "Phylogenetics", + "Metagenomic sequencing" + ], + "Status": "To update", + "Source": "https://github.com/picrust/picrust2/wiki", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "picrust2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/picrust/picrust2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2", + "Galaxy wrapper version": "2.5.1", + "Conda id": "picrust2", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "Phylogenetic reconstruction", + "Expression analysis", + "Rarefaction", + "Pathway analysis" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbiology", + "Phylogenetics", + "Metagenomic sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 7, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pilon", + "Galaxy tool ids": [ + "pilon" + ], + "Description": "pilon is a tool for assembly improvement and variant analysis in bacteria", + "bio.tool id": "pilon", + "bio.tool ids": [ + "pilon" + ], + "biii": null, + "bio.tool name": "pilon", + "bio.tool description": "Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.", + "EDAM operation": [ + "Sequence assembly", + "Analysis", + "Read alignment" + ], + "EDAM topic": [ + "Assembly" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pilon", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon", + "Galaxy wrapper version": "1.20.1", + "Conda id": "pilon", + "Conda version": "1.24", + "EDAM operation (no superclasses)": [ + "Sequence assembly", + "Analysis" + ], + "EDAM topic (no superclasses)": [ + "Assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "pipelign", + "Galaxy tool ids": [ + "pipelign" + ], + "Description": "Multipe sequence alignment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/asmmhossain/pipelign/", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "pipelign", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign", + "Galaxy wrapper version": "0.2", + "Conda id": "pipelign", + "Conda version": "0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pizzly", + "Galaxy tool ids": [ + "pizzly" + ], + "Description": "Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/pmelsted/pizzly/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly", + "Galaxy wrapper version": "0.37.3.1", + "Conda id": "pizzly", + "Conda version": "0.37.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "plasflow", + "Galaxy tool ids": [ + "PlasFlow" + ], + "Description": "PlasFlow - Prediction of plasmid sequences in metagenomic contigs.", + "bio.tool id": "plasflow", + "bio.tool ids": [ + "plasflow" + ], + "biii": null, + "bio.tool name": "PlasFlow", + "bio.tool description": "PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.", + "EDAM operation": [ + "Sequence analysis" + ], + "EDAM topic": [ + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/smaegol/PlasFlow", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "plasflow", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow", + "Galaxy wrapper version": "1.1.0", + "Conda id": "plasflow", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [ + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "plasmidfinder", + "Galaxy tool ids": [ + "plasmidfinder" + ], + "Description": "\"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage\"", + "bio.tool id": "PlasmidFinder", + "bio.tool ids": [ + "PlasmidFinder" + ], + "biii": null, + "bio.tool name": "PlasmidFinder", + "bio.tool description": "PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).", + "EDAM operation": [ + "Genome assembly", + "Scaffolding", + "Multilocus sequence typing" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Sequence assembly", + "Mapping", + "Probes and primers" + ], + "Status": "Up-to-date", + "Source": "https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "plasmidfinder", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder", + "Galaxy wrapper version": "2.1.6", + "Conda id": "plasmidfinder", + "Conda version": "2.1.6", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Scaffolding", + "Multilocus sequence typing" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Sequence assembly", + "Mapping", + "Probes and primers" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "plink", + "Galaxy tool ids": [ + "plink" + ], + "Description": "PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "bio.tool id": "plink", + "bio.tool ids": [ + "plink" + ], + "biii": null, + "bio.tool name": "PLINK", + "bio.tool description": "Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.", + "EDAM operation": [ + "Genetic variation analysis" + ], + "EDAM topic": [ + "GWAS study" + ], + "Status": "Up-to-date", + "Source": "https://www.cog-genomics.org/plink", + "ToolShed categories": [ + "Genome-Wide Association Study" + ], + "ToolShed id": "plink", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink", + "Galaxy wrapper version": "1.90b6.21", + "Conda id": "plink", + "Conda version": "1.90b6.21", + "EDAM operation (no superclasses)": [ + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "GWAS study" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "polypolish", + "Galaxy tool ids": [ + "polypolish" + ], + "Description": "\"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.\"", + "bio.tool id": "Polypolish", + "bio.tool ids": [ + "Polypolish" + ], + "biii": null, + "bio.tool name": "Polypolish", + "bio.tool description": "Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.", + "EDAM operation": [ + "Genome assembly", + "Read mapping", + "Mapping assembly", + "Sequencing error detection" + ], + "EDAM topic": [ + "Sequence assembly", + "Sequence composition, complexity and repeats", + "Mapping" + ], + "Status": "To update", + "Source": "https://github.com/rrwick/Polypolish", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "polypolish", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish", + "Galaxy wrapper version": "0.5.0", + "Conda id": "polypolish", + "Conda version": "0.6.0", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Read mapping", + "Mapping assembly", + "Sequencing error detection" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Sequence composition, complexity and repeats", + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "porechop", + "Galaxy tool ids": [ + "porechop" + ], + "Description": "Porechop - Finding and removing adapters from Oxford Nanopore reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/rrwick/Porechop", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "porechop", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop", + "Galaxy wrapper version": null, + "Conda id": "porechop", + "Conda version": "0.2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "poretools", + "Galaxy tool ids": [ + "poretools_events", + "poretools_extract", + "poretools_hist", + "poretools_nucdist", + "poretools_occupancy", + "poretools_qualdist", + "poretools_qualpos", + "poretools_squiggle", + "poretools_stats", + "poretools_tabular", + "poretools_times", + "poretools_winner", + "poretools_yield_plot" + ], + "Description": "A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.", + "bio.tool id": "poretools", + "bio.tool ids": [ + "poretools" + ], + "biii": null, + "bio.tool name": "Poretools", + "bio.tool description": "Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.", + "EDAM operation": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic": [ + "DNA", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://poretools.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools", + "Galaxy wrapper version": "0.6.1a1", + "Conda id": "poretools", + "Conda version": "0.6.1a1", + "EDAM operation (no superclasses)": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "DNA", + "Sequencing" + ], + "Available on UseGalaxy.org": 13, + "Available on UseGalaxy.org.au": 13, + "Available on UseGalaxy.eu": 13, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "presto", + "Galaxy tool ids": [ + "presto_alignsets", + "presto_assemblepairs", + "presto_buildconsensus", + "presto_collapseseq", + "presto_filterseq", + "presto_maskprimers", + "presto_pairseq", + "presto_parseheaders", + "presto_parselog", + "presto_partition", + "prestor_abseq3" + ], + "Description": "pRESTO toolkit for immune repertoire analysis.", + "bio.tool id": "presto", + "bio.tool ids": [ + "presto" + ], + "biii": null, + "bio.tool name": "pRESTO", + "bio.tool description": "Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.", + "EDAM operation": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic": [ + "Sequencing", + "DNA", + "Immunology" + ], + "Status": "To update", + "Source": "https://presto.readthedocs.io/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "presto", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto", + "Galaxy wrapper version": "0.6.2", + "Conda id": "presto", + "Conda version": "0.7.2", + "EDAM operation (no superclasses)": [ + "Nucleic acid sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "DNA", + "Immunology" + ], + "Available on UseGalaxy.org": 11, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pretext", + "Galaxy tool ids": [ + "pretext_graph", + "pretext_map", + "pretext_snapshot" + ], + "Description": "Process genome contacts maps processing images.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/wtsi-hpag/PretextSnapshot", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "suite_pretext", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext", + "Galaxy wrapper version": "0.0.6", + "Conda id": "pretextgraph", + "Conda version": "0.0.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "prinseq", + "Galaxy tool ids": [ + "prinseq" + ], + "Description": "PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets", + "bio.tool id": "prinseq", + "bio.tool ids": [ + "prinseq" + ], + "biii": null, + "bio.tool name": "PRINSEQ", + "bio.tool description": "PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.", + "EDAM operation": [ + "Read pre-processing", + "Sequence trimming", + "Sequence contamination filtering" + ], + "EDAM topic": [ + "Transcriptomics", + "Metagenomics", + "Genomics" + ], + "Status": "To update", + "Source": "http://prinseq.sourceforge.net/manual.html", + "ToolShed categories": [ + "Fastq Manipulation", + "Metagenomics" + ], + "ToolShed id": "prinseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq", + "Galaxy wrapper version": "@TOOL_VERSION+galaxy2", + "Conda id": "prinseq", + "Conda version": "0.20.4", + "EDAM operation (no superclasses)": [ + "Read pre-processing", + "Sequence trimming", + "Sequence contamination filtering" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Metagenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "prodigal", + "Galaxy tool ids": [ + "prodigal" + ], + "Description": "A protein-coding gene prediction software tool for bacterial and archaeal genomes", + "bio.tool id": "prodigal", + "bio.tool ids": [ + "prodigal" + ], + "biii": null, + "bio.tool name": "Prodigal", + "bio.tool description": "Fast, reliable protein-coding gene prediction for prokaryotic genomes.", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Genomics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/hyattpd/Prodigal", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "prodigal", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal", + "Galaxy wrapper version": "2.6.3", + "Conda id": "prodigal", + "Conda version": "2.6.3", + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "progressivemauve", + "Galaxy tool ids": [ + "progressivemauve", + "xmfa2gff3" + ], + "Description": "Mauve/ProgressiveMauve Multiple Sequence Aligner", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "progressivemauve", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve", + "Galaxy wrapper version": null, + "Conda id": "progressivemauve", + "Conda version": "snapshot_2015_02_13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "prokka", + "Galaxy tool ids": [ + "prokka" + ], + "Description": "Rapid annotation of prokaryotic genomes", + "bio.tool id": "prokka", + "bio.tool ids": [ + "prokka" + ], + "biii": null, + "bio.tool name": "Prokka", + "bio.tool description": "Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.", + "EDAM operation": [ + "Gene prediction", + "Coding region prediction", + "Genome annotation" + ], + "EDAM topic": [ + "Genomics", + "Model organisms", + "Virology" + ], + "Status": "Up-to-date", + "Source": "http://github.com/tseemann/prokka", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "prokka", + "Galaxy wrapper owner": "crs4", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka", + "Galaxy wrapper version": "1.14.6", + "Conda id": "prokka", + "Conda version": "1.14.6", + "EDAM operation (no superclasses)": [ + "Coding region prediction", + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Model organisms", + "Virology" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "prot-scriber", + "Galaxy tool ids": [ + "prot_scriber" + ], + "Description": "Protein annotation of short human readable descriptions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/usadellab/prot-scriber", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "prot_scriber", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber", + "Galaxy wrapper version": "0.1.5", + "Conda id": "prot-scriber", + "Conda version": "0.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteinortho", + "Galaxy tool ids": [ + "proteinortho", + "proteinortho_grab_proteins", + "proteinortho_summary" + ], + "Description": "Proteinortho is a tool to detect orthologous proteins/genes within different species.", + "bio.tool id": "proteinortho", + "bio.tool ids": [ + "proteinortho" + ], + "biii": null, + "bio.tool name": "Proteinortho", + "bio.tool description": "Proteinortho is a tool to detect orthologous genes within different species", + "EDAM operation": [ + "Sequence clustering", + "Sequence analysis" + ], + "EDAM topic": [ + "Comparative genomics" + ], + "Status": "Up-to-date", + "Source": "https://gitlab.com/paulklemm_PHD/proteinortho", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteinortho", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://gitlab.com/paulklemm_PHD/proteinortho", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho", + "Galaxy wrapper version": "6.3.1", + "Conda id": "proteinortho", + "Conda version": "6.3.1", + "EDAM operation (no superclasses)": [ + "Sequence clustering", + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Comparative genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "psiclass", + "Galaxy tool ids": [ + "psiclass" + ], + "Description": "PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.", + "bio.tool id": "psiclass", + "bio.tool ids": [ + "psiclass" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/splicebox/PsiCLASS", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "psiclass", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass", + "Galaxy wrapper version": "1.0.3", + "Conda id": "psiclass", + "Conda version": "1.0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pureclip", + "Galaxy tool ids": [ + "pureclip" + ], + "Description": "PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/skrakau/PureCLIP", + "ToolShed categories": [ + "Sequence Analysis", + "RNA", + "CLIP-seq" + ], + "ToolShed id": "pureclip", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip", + "Galaxy wrapper version": "1.0.4", + "Conda id": "pureclip", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "purge_dups", + "Galaxy tool ids": [ + "purge_dups" + ], + "Description": "Purge haplotigs and overlaps in an assembly based on read depth", + "bio.tool id": "purge_dups", + "bio.tool ids": [ + "purge_dups" + ], + "biii": null, + "bio.tool name": "purge_dups", + "bio.tool description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", + "EDAM operation": [ + "Genome assembly", + "Read binning", + "Scaffolding" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/dfguan/purge_dups", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "purge_dups", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups", + "Galaxy wrapper version": "1.2.6", + "Conda id": "purge_dups", + "Conda version": "1.2.6", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Read binning", + "Scaffolding" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pycoqc", + "Galaxy tool ids": [ + "pycoqc" + ], + "Description": "QC metrics for ONT Basecalling", + "bio.tool id": "pycoqc", + "bio.tool ids": [ + "pycoqc" + ], + "biii": null, + "bio.tool name": "pycoQC", + "bio.tool description": "PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.", + "EDAM operation": [ + "Sequencing quality control", + "Statistical calculation" + ], + "EDAM topic": [ + "Sequence analysis", + "Data quality management", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tleonardi/pycoQC", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "pycoqc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc", + "Galaxy wrapper version": "2.5.2", + "Conda id": "pycoqc", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "Sequencing quality control", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis", + "Data quality management", + "Sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "pyega3", + "Galaxy tool ids": [ + "pyega3" + ], + "Description": "EGA python client uses the EGA REST API to download authorized datasets and files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/EGA-archive/ega-download-client", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "ega_download_client", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3", + "Galaxy wrapper version": "5.0.2", + "Conda id": "pyega3", + "Conda version": "5.2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pygenometracks", + "Galaxy tool ids": [ + "pygenomeTracks" + ], + "Description": "pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.", + "bio.tool id": "pygenometracks", + "bio.tool ids": [ + "pygenometracks" + ], + "biii": null, + "bio.tool name": "pyGenomeTracks", + "bio.tool description": "reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.", + "EDAM operation": [ + "Visualisation", + "Formatting" + ], + "EDAM topic": [ + "Model organisms", + "Imaging", + "Workflows" + ], + "Status": "To update", + "Source": "https://github.com/deeptools/pyGenomeTracks", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "pygenometracks", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks", + "Galaxy wrapper version": "3.8", + "Conda id": "pygenometracks", + "Conda version": "3.9", + "EDAM operation (no superclasses)": [ + "Visualisation", + "Formatting" + ], + "EDAM topic (no superclasses)": [ + "Model organisms", + "Imaging", + "Workflows" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "pysradb", + "Galaxy tool ids": [ + "pysradb_search" + ], + "Description": "pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.", + "bio.tool id": "pysradb", + "bio.tool ids": [ + "pysradb" + ], + "biii": null, + "bio.tool name": "pysradb", + "bio.tool description": "Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.", + "EDAM operation": [ + "Deposition", + "Data retrieval" + ], + "EDAM topic": [ + "Sequencing", + "Gene transcripts", + "Bioinformatics" + ], + "Status": "To update", + "Source": "https://github.com/saketkc/pysradb", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "pysradb_search", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb", + "Galaxy wrapper version": "1.4.2", + "Conda id": "pysradb", + "Conda version": "2.2.0", + "EDAM operation (no superclasses)": [ + "Deposition", + "Data retrieval" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Gene transcripts", + "Bioinformatics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qfilt", + "Galaxy tool ids": [ + "qfilt" + ], + "Description": "Filter sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/veg/qfilt", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "qfilt", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt", + "Galaxy wrapper version": "1.0.0+galaxy1", + "Conda id": "qfilt", + "Conda version": "0.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qiime_add_on", + "Galaxy tool ids": [ + "qiime_collapse_samples", + "qiime_make_otu_table" + ], + "Description": "QIIME to perform microbial community analysis", + "bio.tool id": "qiime_add_on", + "bio.tool ids": [ + "qiime_add_on", + "qiime_core" + ], + "biii": null, + "bio.tool name": "qiime_add_on", + "bio.tool description": "QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.", + "EDAM operation": [ + "Demultiplexing", + "Visualisation", + "Taxonomic classification", + "Phylogenetic analysis", + "Sequencing quality control" + ], + "EDAM topic": [ + "Microbial ecology", + "Phylogeny", + "Metagenomics", + "Metatranscriptomics" + ], + "Status": "To update", + "Source": "http://www.qiime.org", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "qiime", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on", + "Galaxy wrapper version": null, + "Conda id": "qiime", + "Conda version": "1.9.1", + "EDAM operation (no superclasses)": [ + "Demultiplexing", + "Visualisation", + "Taxonomic classification", + "Phylogenetic analysis", + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Microbial ecology", + "Phylogeny", + "Metagenomics", + "Metatranscriptomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "qiime_core", + "Galaxy tool ids": [ + "qiime_align_seqs", + "qiime_alpha_diversity", + "qiime_alpha_rarefaction", + "qiime_assign_taxonomy", + "qiime_beta_diversity", + "qiime_beta_diversity_through_plots", + "qiime_compare_categories", + "qiime_core_diversity", + "qiime_count_seqs", + "qiime_extract_barcodes", + "qiime_filter_alignment", + "qiime_filter_fasta", + "qiime_filter_otus_from_otu_table", + "qiime_filter_samples_from_otu_table", + "qiime_filter_taxa_from_otu_table", + "qiime_jackknifed_beta_diversity", + "qiime_make_emperor", + "qiime_make_otu_heatmap", + "qiime_make_phylogeny", + "qiime_multiple_join_paired_ends", + "qiime_multiple_split_libraries_fastq", + "qiime_pick_closed_reference_otus", + "qiime_pick_open_reference_otus", + "qiime_pick_otus", + "qiime_pick_rep_set", + "qiime_plot_taxa_summary", + "qiime_split_libraries", + "qiime_split_libraries_fastq", + "qiime_summarize_taxa", + "qiime_summarize_taxa_through_plots", + "qiime_upgma_cluster", + "qiime_validate_mapping_file" + ], + "Description": "QIIME to perform microbial community analysis", + "bio.tool id": "qiime_core", + "bio.tool ids": [ + "qiime_core" + ], + "biii": null, + "bio.tool name": "qiime_core", + "bio.tool description": "QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.", + "EDAM operation": [ + "Demultiplexing", + "Visualisation", + "Taxonomic classification", + "Phylogenetic analysis", + "Sequencing quality control" + ], + "EDAM topic": [ + "Microbial ecology", + "Phylogeny", + "Metagenomics", + "Metatranscriptomics" + ], + "Status": "To update", + "Source": "http://www.qiime.org", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "qiime", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core", + "Galaxy wrapper version": null, + "Conda id": "qiime", + "Conda version": "1.9.1", + "EDAM operation (no superclasses)": [ + "Demultiplexing", + "Visualisation", + "Taxonomic classification", + "Phylogenetic analysis", + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Microbial ecology", + "Phylogeny", + "Metagenomics", + "Metatranscriptomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 32, + "Available on UseGalaxy.org.fr": 32 + }, + { + "Galaxy wrapper id": "qiime_extract_viz", + "Galaxy tool ids": [ + "qiime_extract_viz" + ], + "Description": "Extract vizualization from QIIME artifacts", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.qiime.org", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "qiime_extract_viz", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz", + "Galaxy wrapper version": "0.1.0", + "Conda id": "unzip", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qq_tools", + "Galaxy tool ids": [ + "qq_manhattan" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://CRAN.R-project.org/package=qqman", + "ToolShed categories": [ + "Visualization", + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools", + "Galaxy wrapper version": "0.1.0", + "Conda id": "r-qqman", + "Conda version": "0.1.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qualimap", + "Galaxy tool ids": [ + "qualimap_bamqc", + "qualimap_counts", + "qualimap_multi_bamqc", + "qualimap_rnaseq" + ], + "Description": null, + "bio.tool id": "qualimap", + "bio.tool ids": [ + "qualimap" + ], + "biii": null, + "bio.tool name": "QualiMap", + "bio.tool description": "Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.", + "EDAM operation": [ + "Sequencing quality control" + ], + "EDAM topic": [ + "Data quality management" + ], + "Status": "To update", + "Source": "http://qualimap.bioinfo.cipf.es/", + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics", + "SAM" + ], + "ToolShed id": "qualimap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap", + "Galaxy wrapper version": "2.2.2d", + "Conda id": "qualimap", + "Conda version": "2.3", + "EDAM operation (no superclasses)": [ + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Data quality management" + ], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "quast", + "Galaxy tool ids": [ + "quast" + ], + "Description": "Quast (Quality ASsessment Tool) evaluates genome assemblies.", + "bio.tool id": "quast", + "bio.tool ids": [ + "quast" + ], + "biii": null, + "bio.tool name": "QUAST", + "bio.tool description": "QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.", + "EDAM operation": [ + "Visualisation", + "Sequence assembly validation" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "http://quast.bioinf.spbau.ru/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "quast", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast", + "Galaxy wrapper version": "5.2.0", + "Conda id": "quast", + "Conda version": "5.2.0", + "EDAM operation (no superclasses)": [ + "Visualisation", + "Sequence assembly validation" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "query_impc", + "Galaxy tool ids": [ + "query_impc" + ], + "Description": "Contains a tool to query the IMPC database.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc", + "ToolShed categories": [ + "Convert Formats", + "Web Services" + ], + "ToolShed id": "query_impc", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc", + "Galaxy wrapper version": "0.9.0", + "Conda id": "requests", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "query_tabular", + "Galaxy tool ids": [ + "filter_tabular", + "query_tabular", + "sqlite_to_tabular" + ], + "Description": "Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular", + "Galaxy wrapper version": "3.3.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "quickmerge", + "Galaxy tool ids": [ + "quickmerge" + ], + "Description": "Merge long-read and hybrid assemblies to increase contiguity", + "bio.tool id": "quickmerge", + "bio.tool ids": [ + "quickmerge" + ], + "biii": null, + "bio.tool name": "quickmerge", + "bio.tool description": "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.", + "EDAM operation": [ + "Genome assembly", + "Scaffolding", + "De-novo assembly", + "Genotyping" + ], + "EDAM topic": [ + "Structural variation", + "Sequence assembly", + "DNA polymorphism", + "Whole genome sequencing", + "Genotype and phenotype" + ], + "Status": "Up-to-date", + "Source": "https://github.com/mahulchak/quickmerge", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "quickmerge", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge", + "Galaxy wrapper version": "0.3", + "Conda id": "quickmerge", + "Conda version": "0.3", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Scaffolding", + "De-novo assembly", + "Genotyping" + ], + "EDAM topic (no superclasses)": [ + "Structural variation", + "Sequence assembly", + "DNA polymorphism", + "Whole genome sequencing", + "Genotype and phenotype" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "raceid", + "Galaxy tool ids": [ + "raceid_clustering", + "raceid_filtnormconf", + "raceid_inspectclusters", + "raceid_inspecttrajectory", + "raceid_trajectory" + ], + "Description": "RaceID3, StemID2, FateID - scRNA analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/dgrun/RaceID3_StemID2_package/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid", + "Galaxy wrapper version": "0.2.3", + "Conda id": "r-raceid", + "Conda version": "0.1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ragtag", + "Galaxy tool ids": [ + "ragtag" + ], + "Description": "Reference-guided scaffolding of draft genomes tool.", + "bio.tool id": "ragtag", + "bio.tool ids": [ + "ragtag" + ], + "biii": null, + "bio.tool name": "ragtag", + "bio.tool description": "RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/malonge/RagTag", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "ragtag", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag", + "Galaxy wrapper version": "2.1.0", + "Conda id": "ragtag", + "Conda version": "2.1.0", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rapidnj", + "Galaxy tool ids": [ + "rapidnj" + ], + "Description": "Galaxy wrapper for the RapidNJ tool", + "bio.tool id": "rapidnj", + "bio.tool ids": [ + "rapidnj" + ], + "biii": null, + "bio.tool name": "RapidNJ", + "bio.tool description": "A tool for fast canonical neighbor-joining tree construction.", + "EDAM operation": [ + "Phylogenetic tree generation" + ], + "EDAM topic": [ + "Phylogeny" + ], + "Status": "Up-to-date", + "Source": "https://birc.au.dk/software/rapidnj/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "rapidnj", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj", + "Galaxy wrapper version": "2.3.2", + "Conda id": "rapidnj", + "Conda version": "2.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Phylogeny" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rasusa", + "Galaxy tool ids": [ + "rasusa" + ], + "Description": "Randomly subsample sequencing reads to a specified coverage", + "bio.tool id": "rasusa", + "bio.tool ids": [ + "rasusa" + ], + "biii": null, + "bio.tool name": "rasusa", + "bio.tool description": "Produces an unbiased subsample of your reads", + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/mbhall88/rasusa", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "rasusa", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa", + "Galaxy wrapper version": "0.8.0", + "Conda id": "rasusa", + "Conda version": "2.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "raven", + "Galaxy tool ids": [ + "raven" + ], + "Description": "Raven is a de novo genome assembler for long uncorrected reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/lbcb-sci/raven", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven", + "Galaxy wrapper version": "1.8.3", + "Conda id": "raven-assembler", + "Conda version": "1.8.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "raxml", + "Galaxy tool ids": [ + "raxml" + ], + "Description": "RAxML - A Maximum Likelihood based phylogenetic inference", + "bio.tool id": "raxml", + "bio.tool ids": [ + "raxml" + ], + "biii": null, + "bio.tool name": "RAxML", + "bio.tool description": "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.", + "EDAM operation": [ + "Sequence analysis", + "Phylogenetic tree analysis" + ], + "EDAM topic": [ + "Phylogenetics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://www.exelixis-lab.org/web/software/raxml/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "raxml", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml", + "Galaxy wrapper version": "8.2.12", + "Conda id": "raxml", + "Conda version": "8.2.13", + "EDAM operation (no superclasses)": [ + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Phylogenetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rcorrector", + "Galaxy tool ids": [ + "rcorrector" + ], + "Description": "Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.", + "bio.tool id": "rcorrector", + "bio.tool ids": [ + "rcorrector" + ], + "biii": null, + "bio.tool name": "Rcorrector", + "bio.tool description": "This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.", + "EDAM operation": [ + "Sequencing error detection" + ], + "EDAM topic": [ + "RNA", + "RNA-Seq", + "Sequencing" + ], + "Status": "To update", + "Source": "https://github.com/mourisl/Rcorrector", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "rcorrector", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector", + "Galaxy wrapper version": "1.0.3+galaxy1", + "Conda id": "rcorrector", + "Conda version": "1.0.7", + "EDAM operation (no superclasses)": [ + "Sequencing error detection" + ], + "EDAM topic (no superclasses)": [ + "RNA", + "RNA-Seq" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "read_it_and_keep", + "Galaxy tool ids": [ + "read_it_and_keep" + ], + "Description": "Rapid decontamination of SARS-CoV-2 sequencing reads", + "bio.tool id": "read_it_and_keep", + "bio.tool ids": [ + "read_it_and_keep" + ], + "biii": null, + "bio.tool name": "read_it_and_keep", + "bio.tool description": "Read contamination removal", + "EDAM operation": [ + "Filtering", + "Genome alignment" + ], + "EDAM topic": [ + "Pathology", + "Genomics" + ], + "Status": "To update", + "Source": "https://github.com/GenomePathogenAnalysisService/read-it-and-keep", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "read_it_and_keep", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep", + "Galaxy wrapper version": "0.2.2", + "Conda id": "read-it-and-keep", + "Conda version": "0.3.0", + "EDAM operation (no superclasses)": [ + "Filtering", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Pathology", + "Genomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "recentrifuge", + "Galaxy tool ids": [ + "recentrifuge" + ], + "Description": "\"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.\"", + "bio.tool id": "Recentrifuge", + "bio.tool ids": [ + "Recentrifuge" + ], + "biii": null, + "bio.tool name": "Recentrifuge", + "bio.tool description": "Robust comparative analysis and contamination removal for metagenomics.", + "EDAM operation": [ + "Taxonomic classification", + "Expression analysis", + "Cross-assembly" + ], + "EDAM topic": [ + "Metagenomics", + "Microbial ecology", + "Metagenomic sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/khyox/recentrifuge", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "recentrifuge", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge", + "Galaxy wrapper version": "1.14.0", + "Conda id": "recentrifuge", + "Conda version": "1.14.0", + "EDAM operation (no superclasses)": [ + "Taxonomic classification", + "Expression analysis", + "Cross-assembly" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbial ecology", + "Metagenomic sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "red", + "Galaxy tool ids": [ + "red" + ], + "Description": "Red (REpeat Detector)", + "bio.tool id": "red", + "bio.tool ids": [ + "red" + ], + "biii": null, + "bio.tool name": "RED", + "bio.tool description": "This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.", + "EDAM operation": [ + "RNA-Seq analysis", + "Editing" + ], + "EDAM topic": [ + "RNA", + "Sequencing", + "Data visualisation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/BioinformaticsToolsmith/Red", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "red", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/red", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/red", + "Galaxy wrapper version": "2018.09.10", + "Conda id": "red", + "Conda version": "2018.09.10", + "EDAM operation (no superclasses)": [ + "RNA-Seq analysis", + "Editing" + ], + "EDAM topic (no superclasses)": [ + "RNA", + "Sequencing", + "Data visualisation" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "repeatmasker", + "Galaxy tool ids": [ + "repeatmasker_wrapper" + ], + "Description": "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.", + "bio.tool id": "repeatmasker", + "bio.tool ids": [ + "repeatmasker" + ], + "biii": null, + "bio.tool name": "RepeatMasker", + "bio.tool description": "A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).", + "EDAM operation": [ + "Genome annotation" + ], + "EDAM topic": [ + "Sequence analysis", + "Sequence composition, complexity and repeats" + ], + "Status": "Up-to-date", + "Source": "http://www.repeatmasker.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "repeat_masker", + "Galaxy wrapper owner": "bgruening", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker", + "Galaxy wrapper version": "4.1.5", + "Conda id": "repeatmasker", + "Conda version": "4.1.5", + "EDAM operation (no superclasses)": [ + "Genome annotation" + ], + "EDAM topic (no superclasses)": [ + "Sequence composition, complexity and repeats" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "repeatmodeler", + "Galaxy tool ids": [ + "repeatmodeler" + ], + "Description": "RepeatModeler - Model repetitive DNA", + "bio.tool id": "repeatmodeler", + "bio.tool ids": [ + "repeatmodeler" + ], + "biii": null, + "bio.tool name": "RepeatModeler", + "bio.tool description": "De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.", + "EDAM operation": [ + "Repeat sequence detection" + ], + "EDAM topic": [ + "Sequence composition, complexity and repeats", + "Sequence composition, complexity and repeats" + ], + "Status": "To update", + "Source": "https://www.repeatmasker.org/RepeatModeler/", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "repeatmodeler", + "Galaxy wrapper owner": "csbl", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler", + "Galaxy wrapper version": "2.0.5", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Repeat sequence detection" + ], + "EDAM topic (no superclasses)": [ + "Sequence composition, complexity and repeats", + "Sequence composition, complexity and repeats" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "repmatch_gff3", + "Galaxy tool ids": [ + "repmatch_gff3" + ], + "Description": "Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "repmatch_gff3", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3", + "Galaxy wrapper version": null, + "Conda id": "matplotlib", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "reshape2", + "Galaxy tool ids": [ + "cast", + "melt" + ], + "Description": "Flexibly restructure and aggregate data using just the two functions melt and dcast", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cran.r-project.org/web/packages/reshape2/index.html", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2", + "Galaxy wrapper version": "1.4.2", + "Conda id": "r-reshape2", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "resize_coordinate_window", + "Galaxy tool ids": [ + "resize_coordinate_window" + ], + "Description": "Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Genomic Interval Operations" + ], + "ToolShed id": "resize_coordinate_window", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window", + "Galaxy wrapper version": "1.0.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "revoluzer", + "Galaxy tool ids": [ + "revoluzer_crex", + "revoluzer_distmat" + ], + "Description": "revoluzer wrappers", + "bio.tool id": "revoluzer", + "bio.tool ids": [ + "revoluzer" + ], + "biii": null, + "bio.tool name": "revoluzer", + "bio.tool description": "Various tools for genome rearrangement analysis. CREx, TreeREx, etc", + "EDAM operation": [ + "Structural variation detection" + ], + "EDAM topic": [ + "Molecular evolution", + "Phylogeny" + ], + "Status": "Up-to-date", + "Source": "https://gitlab.com/Bernt/revoluzer/", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "revoluzer", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer", + "Galaxy wrapper version": "0.1.6", + "Conda id": "revoluzer", + "Conda version": "0.1.6", + "EDAM operation (no superclasses)": [ + "Structural variation detection" + ], + "EDAM topic (no superclasses)": [ + "Molecular evolution", + "Phylogeny" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rgcca", + "Galaxy tool ids": [ + "rgcca" + ], + "Description": "multi-block analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/rgcca-factory/RGCCA", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "rgcca", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca", + "Galaxy wrapper version": "3.0.2", + "Conda id": "rgccacmd", + "Conda version": "3.0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rgrnastar", + "Galaxy tool ids": [ + "rna_star", + "rna_starsolo" + ], + "Description": "RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper", + "bio.tool id": "star", + "bio.tool ids": [ + "star" + ], + "biii": null, + "bio.tool name": "STAR", + "bio.tool description": "Ultrafast universal RNA-seq data aligner", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "RNA-Seq", + "Transcriptomics" + ], + "Status": "To update", + "Source": "https://github.com/alexdobin/STAR", + "ToolShed categories": [ + "Next Gen Mappers", + "Transcriptomics" + ], + "ToolShed id": "rgrnastar", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar", + "Galaxy wrapper version": "2.7.11a", + "Conda id": "star", + "Conda version": "2.7.11b", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Transcriptomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "ribowaltz", + "Galaxy tool ids": [ + "ribowaltz_process", + "ribowaltz_plot" + ], + "Description": "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data", + "bio.tool id": "riboWaltz", + "bio.tool ids": [ + "riboWaltz" + ], + "biii": null, + "bio.tool name": "riboWaltz", + "bio.tool description": "riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.", + "EDAM operation": [], + "EDAM topic": [ + "Computational biology" + ], + "Status": "To update", + "Source": "https://github.com/LabTranslationalArchitectomics/riboWaltz", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz", + "Galaxy wrapper version": "1.2.0", + "Conda id": "ribowaltz", + "Conda version": "2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Computational biology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rnaquast", + "Galaxy tool ids": [ + "rna_quast" + ], + "Description": "rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.", + "bio.tool id": "rnaQUAST", + "bio.tool ids": [ + "rnaQUAST" + ], + "biii": null, + "bio.tool name": "rnaQUAST", + "bio.tool description": "Quality assessment tool for de novo transcriptome assemblies.", + "EDAM operation": [ + "De-novo assembly", + "Transcriptome assembly", + "Sequence assembly validation" + ], + "EDAM topic": [ + "Sequence assembly", + "Transcriptomics", + "RNA-seq" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ablab/rnaquast", + "ToolShed categories": [ + "Assembly", + "RNA" + ], + "ToolShed id": "rnaquast", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://git.ufz.de/lehmanju/rnaquast", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast", + "Galaxy wrapper version": "2.2.3", + "Conda id": "rnaquast", + "Conda version": "2.2.3", + "EDAM operation (no superclasses)": [ + "De-novo assembly", + "Transcriptome assembly", + "Sequence assembly validation" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Transcriptomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "roary", + "Galaxy tool ids": [ + "roary" + ], + "Description": "Roary the pangenome pipeline", + "bio.tool id": "roary", + "bio.tool ids": [ + "roary" + ], + "biii": null, + "bio.tool name": "Roary", + "bio.tool description": "A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "DNA", + "Genomics", + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://sanger-pathogens.github.io/Roary/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "roary", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary", + "Galaxy wrapper version": "3.13.0", + "Conda id": "roary", + "Conda version": "3.13.0", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "DNA", + "Genomics", + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rp2biosensor", + "Galaxy tool ids": [ + "rp2biosensor" + ], + "Description": "Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/rp2biosensor", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rp2biosensor", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor", + "Galaxy wrapper version": "3.2.1", + "Conda id": "rp2biosensor", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rp2paths", + "Galaxy tool ids": [ + "rp2paths" + ], + "Description": "Enumerate and seperate the different pathways generated by RetroPath2.0", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/rp2paths", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rp2paths", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths", + "Galaxy wrapper version": "1.5.1", + "Conda id": "rp2paths", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rpbasicdesign", + "Galaxy tool ids": [ + "rpbasicdesign" + ], + "Description": "Extracting enzyme IDs from rpSBML files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/rpbasicdesign", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rpbasicdesign", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign", + "Galaxy wrapper version": "1.2.2", + "Conda id": "rpbasicdesign", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rpfba", + "Galaxy tool ids": [ + "rpfba" + ], + "Description": "Perform FBA for the RetroPath2.0 heterologous pathways", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/rptools/releases", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rpfba", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba", + "Galaxy wrapper version": "5.12.3", + "Conda id": "rptools", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rptools", + "Galaxy tool ids": [ + "rptools_rpextractsink", + "rptools_rpfba", + "rptools_rpranker", + "rptools_rpreport", + "rptools_rpviz" + ], + "Description": "Suite of tools that work on rpSBML format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/rptools", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rptools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools", + "Galaxy wrapper version": "5.13.1", + "Conda id": "rptools", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rrparser", + "Galaxy tool ids": [ + "rrparser" + ], + "Description": "Reaction Rules Parser", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/RRParser", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "rrparser", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser", + "Galaxy wrapper version": "2.5.2", + "Conda id": "rrparser", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rseqc", + "Galaxy tool ids": [ + "rseqc_FPKM_count", + "rseqc_RNA_fragment_size", + "rseqc_RPKM_saturation", + "rseqc_bam2wig", + "rseqc_bam_stat", + "rseqc_clipping_profile", + "rseqc_deletion_profile", + "rseqc_geneBody_coverage", + "rseqc_geneBody_coverage2", + "rseqc_infer_experiment", + "rseqc_inner_distance", + "rseqc_insertion_profile", + "rseqc_junction_annotation", + "rseqc_junction_saturation", + "rseqc_mismatch_profile", + "rseqc_read_GC", + "rseqc_read_NVC", + "rseqc_read_distribution", + "rseqc_read_duplication", + "rseqc_read_hexamer", + "rseqc_read_quality", + "rseqc_tin" + ], + "Description": "an RNA-seq quality control package", + "bio.tool id": "rseqc", + "bio.tool ids": [ + "rseqc" + ], + "biii": null, + "bio.tool name": "RSeQC", + "bio.tool description": "Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.", + "EDAM operation": [ + "Data handling" + ], + "EDAM topic": [ + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://code.google.com/p/rseqc/", + "ToolShed categories": [ + "Convert Formats", + "Sequence Analysis", + "RNA", + "Transcriptomics", + "Visualization" + ], + "ToolShed id": "rseqc", + "Galaxy wrapper owner": "nilesh", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc", + "Galaxy wrapper version": "5.0.3", + "Conda id": "rseqc", + "Conda version": "5.0.3", + "EDAM operation (no superclasses)": [ + "Data handling" + ], + "EDAM topic (no superclasses)": [ + "Sequencing" + ], + "Available on UseGalaxy.org": 22, + "Available on UseGalaxy.org.au": 22, + "Available on UseGalaxy.eu": 22, + "Available on UseGalaxy.org.fr": 22 + }, + { + "Galaxy wrapper id": "ruvseq", + "Galaxy tool ids": [ + "ruvseq" + ], + "Description": "Remove Unwanted Variation from RNA-Seq Data", + "bio.tool id": "ruvseq", + "bio.tool ids": [ + "ruvseq" + ], + "biii": null, + "bio.tool name": "RUVSeq", + "bio.tool description": "This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.", + "EDAM operation": [ + "Differential gene expression analysis" + ], + "EDAM topic": [ + "Gene expression", + "RNA-seq" + ], + "Status": "To update", + "Source": "https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "ruvseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq", + "Galaxy wrapper version": "1.26.0", + "Conda id": "bioconductor-ruvseq", + "Conda version": "1.36.0", + "EDAM operation (no superclasses)": [ + "Differential gene expression analysis" + ], + "EDAM topic (no superclasses)": [ + "Gene expression" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "salsa2", + "Galaxy tool ids": [ + "salsa" + ], + "Description": "A tool to scaffold long read assemblies with Hi-C", + "bio.tool id": "SALSA", + "bio.tool ids": [ + "SALSA" + ], + "biii": null, + "bio.tool name": "SALSA", + "bio.tool description": "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch", + "EDAM operation": [ + "Genome assembly", + "De-novo assembly", + "Scaffolding" + ], + "EDAM topic": [ + "Sequence assembly", + "DNA binding sites", + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/SALSA", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "salsa", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2", + "Galaxy wrapper version": "2.3", + "Conda id": "salsa2", + "Conda version": "2.3", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "De-novo assembly", + "Scaffolding" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "DNA binding sites", + "Mapping" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "samblaster", + "Galaxy tool ids": [ + "samblaster" + ], + "Description": "samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files", + "bio.tool id": "samblaster", + "bio.tool ids": [ + "samblaster" + ], + "biii": null, + "bio.tool name": "SAMBLASTER", + "bio.tool description": "A tool to mark duplicates and extract discordant and split reads from SAM files.", + "EDAM operation": [ + "Split read mapping" + ], + "EDAM topic": [ + "DNA", + "Sequencing", + "Mapping" + ], + "Status": "To update", + "Source": "https://github.com/GregoryFaust/samblaster", + "ToolShed categories": [ + "SAM", + "Fastq Manipulation", + "Variant Analysis" + ], + "ToolShed id": "samblaster", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster", + "Galaxy wrapper version": "0.1.24", + "Conda id": "samblaster", + "Conda version": "0.1.26", + "EDAM operation (no superclasses)": [ + "Split read mapping" + ], + "EDAM topic (no superclasses)": [ + "DNA", + "Sequencing", + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sansa", + "Galaxy tool ids": [ + "sansa_annotate" + ], + "Description": "Sansa is a tool for structural variant annotation.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/dellytools/sansa", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "sansa", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa", + "Galaxy wrapper version": "0.2.1", + "Conda id": "sansa", + "Conda version": "0.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sarscov2formatter", + "Galaxy tool ids": [ + "sarscov2formatter" + ], + "Description": "sarscov2formatter custom script", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/nickeener/sarscov2formatter", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sarscov2formatter", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter", + "Galaxy wrapper version": "1.0", + "Conda id": "sarscov2formatter", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sarscov2summary", + "Galaxy tool ids": [ + "sarscov2summary" + ], + "Description": "sarscov2summary custom script", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nickeener/sarscov2summary", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sarscov2summary", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary", + "Galaxy wrapper version": "0.1", + "Conda id": "sarscov2summary", + "Conda version": "0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sbml2sbol", + "Galaxy tool ids": [ + "sbml2sbol" + ], + "Description": "Convert SBML to SBOL format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/neilswainston/SbmlToSbol", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "sbml2sbol", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol", + "Galaxy wrapper version": "0.1.13", + "Conda id": "sbml2sbol", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scanpy", + "Galaxy tool ids": [ + "scanpy_cluster_reduce_dimension", + "scanpy_filter", + "scanpy_inspect", + "scanpy_normalize", + "scanpy_plot", + "scanpy_remove_confounders" + ], + "Description": "Scanpy – Single-Cell Analysis in Python", + "bio.tool id": "scanpy", + "bio.tool ids": [ + "scanpy" + ], + "biii": null, + "bio.tool name": "SCANPY", + "bio.tool description": "Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.", + "EDAM operation": [ + "Differential gene expression analysis" + ], + "EDAM topic": [ + "Gene expression", + "Cell biology", + "Genetics" + ], + "Status": "To update", + "Source": "https://scanpy.readthedocs.io", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "scanpy", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy", + "Galaxy wrapper version": "1.9.6", + "Conda id": "scanpy", + "Conda version": "1.7.2", + "EDAM operation (no superclasses)": [ + "Differential gene expression analysis" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "Cell biology", + "Genetics" + ], + "Available on UseGalaxy.org": 6, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scater", + "Galaxy tool ids": [ + "scater_create_qcmetric_ready_sce", + "scater_filter", + "scater_plot_dist_scatter", + "scater_plot_pca", + "scater_plot_tsne" + ], + "Description": "Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.", + "bio.tool id": "scater", + "bio.tool ids": [ + "scater" + ], + "biii": null, + "bio.tool name": "scater", + "bio.tool description": "Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.", + "EDAM operation": [ + "Read pre-processing", + "Sequencing quality control", + "Sequence visualisation" + ], + "EDAM topic": [ + "RNA-seq", + "Quality affairs", + "Molecular genetics" + ], + "Status": "To update", + "Source": "http://bioconductor.org/packages/scater/", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Visualization" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater", + "Galaxy wrapper version": "1.22.0", + "Conda id": "bioconductor-scater", + "Conda version": "1.30.1", + "EDAM operation (no superclasses)": [ + "Read pre-processing", + "Sequence visualisation" + ], + "EDAM topic (no superclasses)": [ + "Quality affairs", + "Molecular genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sceasy", + "Galaxy tool ids": [ + "sceasy_convert" + ], + "Description": "Converter between difference single-cell formats", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/cellgeni/sceasy/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "sceasy_convert", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy", + "Galaxy wrapper version": "0.0.7", + "Conda id": "r-sceasy", + "Conda version": "0.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "schicexplorer", + "Galaxy tool ids": [ + "schicexplorer_schicadjustmatrix", + "schicexplorer_schiccluster", + "schicexplorer_schicclustercompartments", + "schicexplorer_schicclusterminhash", + "schicexplorer_schicclustersvl", + "schicexplorer_schicconsensusmatrices", + "schicexplorer_schiccorrectmatrices", + "schicexplorer_schiccreatebulkmatrix", + "schicexplorer_schicdemultiplex", + "schicexplorer_schicinfo", + "schicexplorer_schicmergematrixbins", + "schicexplorer_schicmergetoscool", + "schicexplorer_schicnormalize", + "schicexplorer_schicplotclusterprofiles", + "schicexplorer_schicplotconsensusmatrices", + "schicexplorer_schicqualitycontrol" + ], + "Description": "scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/joachimwolff/schicexplorer", + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics", + "Visualization" + ], + "ToolShed id": "schicexplorer", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer", + "Galaxy wrapper version": "4", + "Conda id": "schicexplorer", + "Conda version": "7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 16, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scikit-bio", + "Galaxy tool ids": [ + "scikit_bio_diversity_beta_diversity" + ], + "Description": "scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://scikit-bio.org/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "scikit_bio", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio", + "Galaxy wrapper version": "0.4.2", + "Conda id": "scikit-bio", + "Conda version": "0.4.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scoary", + "Galaxy tool ids": [ + "scoary" + ], + "Description": "Scoary calculates the assocations between all genes in the accessory genome and the traits.", + "bio.tool id": "scoary", + "bio.tool ids": [ + "scoary" + ], + "biii": null, + "bio.tool name": "Scoary", + "bio.tool description": "Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.", + "EDAM operation": [ + "Analysis" + ], + "EDAM topic": [ + "Genotype and phenotype", + "Model organisms", + "GWAS study", + "Functional genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/AdmiralenOla/Scoary", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "scoary", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary", + "Galaxy wrapper version": "1.6.16", + "Conda id": "scoary", + "Conda version": "1.6.16", + "EDAM operation (no superclasses)": [ + "Analysis" + ], + "EDAM topic (no superclasses)": [ + "Genotype and phenotype", + "Model organisms", + "GWAS study", + "Functional genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scpipe", + "Galaxy tool ids": [ + "scpipe" + ], + "Description": "A flexible preprocessing pipeline for single-cell RNA-sequencing data", + "bio.tool id": "scpipe", + "bio.tool ids": [ + "scpipe" + ], + "biii": null, + "bio.tool name": "scPipe", + "bio.tool description": "A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.", + "EDAM operation": [ + "Genome annotation", + "Validation", + "Alignment", + "Visualisation" + ], + "EDAM topic": [ + "Gene expression", + "RNA-Seq", + "Sequencing" + ], + "Status": "To update", + "Source": "http://bioconductor.org/packages/release/bioc/html/scPipe.html", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "scpipe", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe", + "Galaxy wrapper version": "1.0.0+galaxy2", + "Conda id": "bioconductor-scpipe", + "Conda version": "2.2.0", + "EDAM operation (no superclasses)": [ + "Genome annotation", + "Validation", + "Alignment", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "RNA-Seq" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seacr", + "Galaxy tool ids": [ + "seacr" + ], + "Description": "SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/FredHutch/SEACR", + "ToolShed categories": [ + "Epigenetics", + "ChIP-seq" + ], + "ToolShed id": "seacr", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr", + "Galaxy wrapper version": "1.3", + "Conda id": "seacr", + "Conda version": "1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "selenzy_wrapper", + "Galaxy tool ids": [ + "selenzy_wrapper" + ], + "Description": "Performs enzyme selection from a reaction query.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/brsynth/selenzy-wrapper", + "ToolShed categories": [ + "Synthetic Biology" + ], + "ToolShed id": "selenzy_wrapper", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper", + "Galaxy wrapper version": "0.3.0", + "Conda id": "selenzy_wrapper", + "Conda version": "0.3.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "semibin", + "Galaxy tool ids": [ + "semibin_bin", + "semibin_concatenate_fasta", + "semibin_generate_cannot_links", + "semibin_generate_sequence_features", + "semibin", + "semibin_train" + ], + "Description": "SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks", + "bio.tool id": "semibin", + "bio.tool ids": [ + "semibin" + ], + "biii": null, + "bio.tool name": "SemiBin", + "bio.tool description": "Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.", + "EDAM operation": [ + "Sequence assembly", + "Read binning" + ], + "EDAM topic": [ + "Metagenomics", + "Machine learning", + "Microbial ecology", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://semibin.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "semibin", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin", + "Galaxy wrapper version": "2.0.2", + "Conda id": "semibin", + "Conda version": "2.1.0", + "EDAM operation (no superclasses)": [ + "Sequence assembly", + "Read binning" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Machine learning", + "Microbial ecology", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "seq2hla", + "Galaxy tool ids": [ + "seq2hla" + ], + "Description": "Precision HLA typing and expression from RNAseq data", + "bio.tool id": "seq2hla", + "bio.tool ids": [ + "seq2hla" + ], + "biii": null, + "bio.tool name": "Seq2HLA", + "bio.tool description": "seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.", + "EDAM operation": [ + "Read mapping", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Transcriptomics", + "Mapping" + ], + "Status": "Up-to-date", + "Source": "https://github.com/TRON-Bioinformatics/seq2HLA", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seq2hla", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla", + "Galaxy wrapper version": "2.3", + "Conda id": "seq2hla", + "Conda version": "2.3", + "EDAM operation (no superclasses)": [ + "Read mapping", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Mapping" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seqcomplexity", + "Galaxy tool ids": [ + "seqcomplexity" + ], + "Description": "Sequence complexity for raw reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/stevenweaver/seqcomplexity", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity", + "Galaxy wrapper version": "0.1.2", + "Conda id": "seqcomplexity", + "Conda version": "0.1.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seqkit", + "Galaxy tool ids": [ + "seqkit_fx2tab", + "seqkit_locate", + "seqkit_sort", + "seqkit_stats", + "seqkit_translate" + ], + "Description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation", + "bio.tool id": "seqkit", + "bio.tool ids": [ + "seqkit" + ], + "biii": null, + "bio.tool name": "seqkit", + "bio.tool description": "FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.", + "EDAM operation": [ + "DNA transcription", + "Sequence trimming", + "DNA translation", + "Sequence conversion" + ], + "EDAM topic": [ + "Database management", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://bioinf.shenwei.me/seqkit/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit", + "Galaxy wrapper version": "2.8.2", + "Conda id": "seqkit", + "Conda version": "2.8.2", + "EDAM operation (no superclasses)": [ + "DNA transcription", + "Sequence trimming", + "DNA translation" + ], + "EDAM topic (no superclasses)": [ + "Database management", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "seqprep", + "Galaxy tool ids": [ + "seqprep" + ], + "Description": "Tool for merging paired-end Illumina reads and trimming adapters.", + "bio.tool id": "seqprep", + "bio.tool ids": [ + "seqprep" + ], + "biii": null, + "bio.tool name": "SeqPrep", + "bio.tool description": "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.", + "EDAM operation": [ + "Nucleic acid design" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly", + "Sequencing", + "Probes and primers" + ], + "Status": "Up-to-date", + "Source": "https://github.com/jstjohn/SeqPrep", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "seqprep", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep", + "Galaxy wrapper version": "1.3.2", + "Conda id": "seqprep", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [ + "Nucleic acid design" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly", + "Sequencing", + "Probes and primers" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seqsero2", + "Galaxy tool ids": [ + "seqsero2" + ], + "Description": "Salmonella serotype prediction from genome sequencing data", + "bio.tool id": "seqsero2", + "bio.tool ids": [ + "seqsero2" + ], + "biii": null, + "bio.tool name": "SeqSero2", + "bio.tool description": "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)", + "EDAM operation": [ + "Genome indexing", + "Antimicrobial resistance prediction", + "Genome alignment" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Sequence assembly", + "Genomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/denglab/SeqSero2", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqsero2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2", + "Galaxy wrapper version": "1.3.1", + "Conda id": "seqsero2", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [ + "Genome indexing", + "Antimicrobial resistance prediction", + "Genome alignment" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Sequence assembly", + "Genomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seqtk", + "Galaxy tool ids": [ + "seqtk_comp", + "seqtk_cutN", + "seqtk_dropse", + "seqtk_fqchk", + "seqtk_hety", + "seqtk_listhet", + "seqtk_mergefa", + "seqtk_mergepe", + "seqtk_mutfa", + "seqtk_randbase", + "seqtk_sample", + "seqtk_seq", + "seqtk_subseq", + "seqtk_telo", + "seqtk_trimfq" + ], + "Description": "Toolkit for processing sequences in FASTA/Q formats", + "bio.tool id": "seqtk", + "bio.tool ids": [ + "seqtk" + ], + "biii": null, + "bio.tool name": "seqtk", + "bio.tool description": "A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.", + "EDAM operation": [ + "Data handling", + "Sequence file editing" + ], + "EDAM topic": [ + "Data management" + ], + "Status": "Up-to-date", + "Source": "https://github.com/lh3/seqtk", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "seqtk", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk", + "Galaxy wrapper version": "1.4", + "Conda id": "seqtk", + "Conda version": "1.4", + "EDAM operation (no superclasses)": [ + "Data handling", + "Sequence file editing" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 15, + "Available on UseGalaxy.org.au": 15, + "Available on UseGalaxy.eu": 15, + "Available on UseGalaxy.org.fr": 15 + }, + { + "Galaxy wrapper id": "seqwish", + "Galaxy tool ids": [ + "seqwish" + ], + "Description": "Alignment to variation graph inducer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/seqwish", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish", + "Galaxy wrapper version": "0.7.5", + "Conda id": "seqwish", + "Conda version": "0.7.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seurat", + "Galaxy tool ids": [ + "seurat" + ], + "Description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/satijalab/seurat", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "seurat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat", + "Galaxy wrapper version": "4.3.0.1", + "Conda id": "r-seurat", + "Conda version": "3.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "shasta", + "Galaxy tool ids": [ + "shasta" + ], + "Description": "Fast de novo assembly of long read sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/chanzuckerberg/shasta", + "ToolShed categories": [ + "Assembly", + "Nanopore" + ], + "ToolShed id": "shasta", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta", + "Galaxy wrapper version": "0.6.0", + "Conda id": "shasta", + "Conda version": "0.12.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "shorah", + "Galaxy tool ids": [ + "shorah_amplicon" + ], + "Description": "Reconstruct haplotypes using ShoRAH in amplicon mode", + "bio.tool id": "shorah", + "bio.tool ids": [ + "shorah" + ], + "biii": null, + "bio.tool name": "ShoRAH", + "bio.tool description": "Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.", + "EDAM operation": [ + "Haplotype mapping", + "Variant calling" + ], + "EDAM topic": [ + "Metagenomics", + "Sequencing", + "Genetics" + ], + "Status": "To update", + "Source": "https://github.com/cbg-ethz/shorah/blob/master/README.md", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "shorah_amplicon", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah", + "Galaxy wrapper version": "1.1.3", + "Conda id": "shorah", + "Conda version": "1.99.2", + "EDAM operation (no superclasses)": [ + "Haplotype mapping", + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequencing", + "Genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "shovill", + "Galaxy tool ids": [ + "shovill" + ], + "Description": "Faster de novo assembly pipeline based around Spades", + "bio.tool id": "shovill", + "bio.tool ids": [ + "shovill" + ], + "biii": null, + "bio.tool name": "shovill", + "bio.tool description": "Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Genomics", + "Microbiology", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/shovill", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "shovill", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill", + "Galaxy wrapper version": "1.1.0", + "Conda id": "shovill", + "Conda version": "1.1.0", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Microbiology", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "sickle", + "Galaxy tool ids": [ + "sickle" + ], + "Description": "A windowed adaptive trimming tool for FASTQ files using quality", + "bio.tool id": "sickle", + "bio.tool ids": [ + "sickle" + ], + "biii": null, + "bio.tool name": "sickle", + "bio.tool description": "A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.", + "EDAM operation": [ + "Sequence trimming" + ], + "EDAM topic": [ + "Data quality management" + ], + "Status": "To update", + "Source": "https://github.com/najoshi/sickle", + "ToolShed categories": [ + "Fastq Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "sickle", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle", + "Galaxy wrapper version": "1.33.2", + "Conda id": "sickle-trim", + "Conda version": "1.33", + "EDAM operation (no superclasses)": [ + "Sequence trimming" + ], + "EDAM topic (no superclasses)": [ + "Data quality management" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "simtext", + "Galaxy tool ids": [ + "abstracts_by_pmids", + "pmids_to_pubtator_matrix", + "pubmed_by_queries", + "text_to_wordmatrix" + ], + "Description": "A text mining framework for interactive analysis and visualization of similarities among biomedical entities.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/dlal-group/simtext", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "simtext", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tools/simtext", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext", + "Galaxy wrapper version": "0.0.2", + "Conda id": "r-argparse", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sina", + "Galaxy tool ids": [ + "sina" + ], + "Description": "SINA reference based multiple sequence alignment", + "bio.tool id": "sina", + "bio.tool ids": [ + "sina" + ], + "biii": null, + "bio.tool name": "SINA", + "bio.tool description": "Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment", + "EDAM operation": [ + "Sequence alignment analysis", + "Multiple sequence alignment", + "Taxonomic classification", + "Structure-based sequence alignment" + ], + "EDAM topic": [ + "Sequencing", + "RNA", + "Nucleic acid structure analysis", + "Taxonomy", + "Sequence analysis", + "Taxonomy" + ], + "Status": "Up-to-date", + "Source": "https://sina.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sina", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina", + "Galaxy wrapper version": "1.7.2", + "Conda id": "sina", + "Conda version": "1.7.2", + "EDAM operation (no superclasses)": [ + "Sequence alignment analysis", + "Multiple sequence alignment", + "Taxonomic classification", + "Structure-based sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "RNA", + "Nucleic acid structure analysis", + "Taxonomy", + "Sequence analysis", + "Taxonomy" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sinto", + "Galaxy tool ids": [ + "sinto_barcode", + "sinto_fragments" + ], + "Description": "Sinto single-cell analysis tools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/timoast/sinto", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto", + "Galaxy wrapper version": "0.9.0", + "Conda id": "sinto", + "Conda version": "0.10.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "slamdunk", + "Galaxy tool ids": [ + "alleyoop", + "slamdunk" + ], + "Description": "Slamdunk maps and quantifies SLAMseq reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://t-neumann.github.io/slamdunk", + "ToolShed categories": [ + "RNA", + "Transcriptomics", + "Sequence Analysis", + "Next Gen Mappers" + ], + "ToolShed id": "slamdunk", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk", + "Galaxy wrapper version": "0.4.3", + "Conda id": "slamdunk", + "Conda version": "0.4.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sleuth", + "Galaxy tool ids": [ + "sleuth" + ], + "Description": "Sleuth is a program for differential analysis of RNA-Seq data.", + "bio.tool id": "sleuth", + "bio.tool ids": [ + "sleuth" + ], + "biii": null, + "bio.tool name": "sleuth", + "bio.tool description": "A statistical model and software application for RNA-seq differential expression analysis.", + "EDAM operation": [ + "Expression data visualisation", + "Differential gene expression analysis", + "Gene expression profiling", + "Statistical calculation" + ], + "EDAM topic": [ + "RNA-seq", + "Gene expression", + "Statistics and probability" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pachterlab/sleuth", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "sleuth", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth", + "Galaxy wrapper version": "0.30.1", + "Conda id": "r-sleuth", + "Conda version": "0.30.1", + "EDAM operation (no superclasses)": [ + "Expression data visualisation", + "Differential gene expression analysis", + "Gene expression profiling", + "Statistical calculation" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "smallgenomeutilities", + "Galaxy tool ids": [ + "smgu_frameshift_deletions_checks" + ], + "Description": "Set of utilities for manipulating small viral genome data.", + "bio.tool id": "v-pipe", + "bio.tool ids": [ + "v-pipe" + ], + "biii": null, + "bio.tool name": "V-pipe", + "bio.tool description": "Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.", + "EDAM operation": [ + "Read pre-processing", + "Sequence alignment", + "Genetic variation analysis" + ], + "EDAM topic": [ + "Genomics", + "Population genetics", + "Workflows", + "Virology", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/cbg-ethz/smallgenomeutilities", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "smallgenomeutilities", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities", + "Galaxy wrapper version": "0.4.1", + "Conda id": "smallgenomeutilities", + "Conda version": "0.4.1", + "EDAM operation (no superclasses)": [ + "Read pre-processing", + "Sequence alignment", + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Population genetics", + "Workflows", + "Virology", + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "smudgeplot", + "Galaxy tool ids": [ + "smudgeplot" + ], + "Description": "Inference of ploidy and heterozygosity structure using whole genome sequencing", + "bio.tool id": "smudgeplots", + "bio.tool ids": [ + "smudgeplots" + ], + "biii": null, + "bio.tool name": "Smudgeplots", + "bio.tool description": "Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568", + "EDAM operation": [ + "Sequence trimming", + "Genotyping", + "k-mer counting" + ], + "EDAM topic": [ + "Sequence assembly", + "Genetic variation", + "Mathematics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/KamilSJaron/smudgeplot", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "smudgeplot", + "Galaxy wrapper owner": "galaxy-australia", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot", + "Galaxy wrapper version": "0.2.5", + "Conda id": "smudgeplot", + "Conda version": "0.2.5", + "EDAM operation (no superclasses)": [ + "Sequence trimming", + "Genotyping", + "k-mer counting" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly", + "Genetic variation", + "Mathematics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snap", + "Galaxy tool ids": [ + "snap", + "snap_training" + ], + "Description": "SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.", + "bio.tool id": "snap", + "bio.tool ids": [ + "snap" + ], + "biii": null, + "bio.tool name": "SNAP", + "bio.tool description": "The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.", + "EDAM operation": [ + "Gene prediction" + ], + "EDAM topic": [ + "DNA", + "DNA polymorphism", + "Genetics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/KorfLab/SNAP", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "snap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap", + "Galaxy wrapper version": "2013_11_29", + "Conda id": "snap", + "Conda version": "2013_11_29", + "EDAM operation (no superclasses)": [ + "Gene prediction" + ], + "EDAM topic (no superclasses)": [ + "DNA polymorphism", + "Genetics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snapatac2", + "Galaxy tool ids": [ + "snapatac2_clustering", + "snapatac2_peaks_and_motif", + "snapatac2_plotting", + "snapatac2_preprocessing" + ], + "Description": "SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://kzhang.org/SnapATAC2/", + "ToolShed categories": [ + "Epigenetics", + "Sequence Analysis" + ], + "ToolShed id": "snapatac2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2", + "Galaxy wrapper version": "2.5.3", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sniffles", + "Galaxy tool ids": [ + "sniffles" + ], + "Description": "Galaxy wrapper for sniffles", + "bio.tool id": "sniffles", + "bio.tool ids": [ + "sniffles" + ], + "biii": null, + "bio.tool name": "Sniffles", + "bio.tool description": "An algorithm for structural variation detection from third generation sequencing alignment.", + "EDAM operation": [ + "Sequence analysis", + "Structural variation detection" + ], + "EDAM topic": [ + "DNA structural variation", + "Sequencing" + ], + "Status": "To update", + "Source": "https://github.com/fritzsedlazeck/Sniffles", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sniffles", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles", + "Galaxy wrapper version": "1.0.12", + "Conda id": "sniffles", + "Conda version": "2.3.3", + "EDAM operation (no superclasses)": [ + "Sequence analysis", + "Structural variation detection" + ], + "EDAM topic (no superclasses)": [ + "Sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "snipit", + "Galaxy tool ids": [ + "snipit" + ], + "Description": "Summarise snps relative to a reference sequence", + "bio.tool id": "snipit", + "bio.tool ids": [ + "snipit" + ], + "biii": null, + "bio.tool name": "snipit", + "bio.tool description": "Summarise snps relative to a reference sequence", + "EDAM operation": [ + "Base position variability plotting" + ], + "EDAM topic": [ + "Virology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/aineniamh/snipit", + "ToolShed categories": [ + "Variant Analysis", + "Sequence Analysis" + ], + "ToolShed id": "snipit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit", + "Galaxy wrapper version": "1.2", + "Conda id": "snipit", + "Conda version": "1.2", + "EDAM operation (no superclasses)": [ + "Base position variability plotting" + ], + "EDAM topic (no superclasses)": [ + "Virology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snippy", + "Galaxy tool ids": [ + "snippy_core", + "snippy", + "snippy_clean_full_aln" + ], + "Description": "Contains the snippy tool for characterising microbial snps", + "bio.tool id": "snippy", + "bio.tool ids": [ + "snippy" + ], + "biii": null, + "bio.tool name": "snippy", + "bio.tool description": "Rapid haploid variant calling and core SNP phylogeny generation.", + "EDAM operation": [ + "Phylogenetic tree visualisation", + "Phylogenetic tree generation", + "Variant calling" + ], + "EDAM topic": [ + "Genomics", + "Model organisms", + "DNA polymorphism", + "Phylogenetics" + ], + "Status": "To update", + "Source": "https://github.com/tseemann/snippy", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "snippy", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy", + "Galaxy wrapper version": null, + "Conda id": "snippy", + "Conda version": "4.6.0", + "EDAM operation (no superclasses)": [ + "Phylogenetic tree visualisation", + "Variant calling" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Model organisms", + "DNA polymorphism", + "Phylogenetics" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "snp-dists", + "Galaxy tool ids": [ + "snp_dists" + ], + "Description": "Compute pairwise SNP distance matrix from a FASTA sequence alignment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/tseemann/snp-dists", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snp_dists", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists", + "Galaxy wrapper version": "0.8.2", + "Conda id": "snp-dists", + "Conda version": "0.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snp-sites", + "Galaxy tool ids": [ + "snp_sites" + ], + "Description": "Finds SNP sites from a multi-FASTA alignment file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/sanger-pathogens/snp-sites", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snp_sites", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites", + "Galaxy wrapper version": "2.5.1", + "Conda id": "snp-sites", + "Conda version": "2.5.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snpeff-covid19", + "Galaxy tool ids": [ + "snpeff_sars_cov_2" + ], + "Description": "SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox", + "bio.tool id": "snpeff", + "bio.tool ids": [ + "snpeff" + ], + "biii": null, + "bio.tool name": "snpEff", + "bio.tool description": "Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).", + "EDAM operation": [ + "SNP detection" + ], + "EDAM topic": [ + "DNA polymorphism", + "Genetic variation", + "Nucleic acid sites, features and motifs" + ], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/", + "ToolShed categories": [ + "Genome-Wide Association Study", + "Variant Analysis" + ], + "ToolShed id": "snpeff_sars_cov_2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "SNP detection" + ], + "EDAM topic (no superclasses)": [ + "DNA polymorphism", + "Nucleic acid sites, features and motifs" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "snpfreqplot", + "Galaxy tool ids": [ + "snpfreqplot" + ], + "Description": "Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snpfreqplot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot", + "Galaxy wrapper version": "1.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "socru", + "Galaxy tool ids": [ + "socru" + ], + "Description": "Order and orientation of complete bacterial genomes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/quadram-institute-bioscience/socru", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "socru", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru", + "Galaxy wrapper version": "2.1.7", + "Conda id": "socru", + "Conda version": "2.2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sonneityping", + "Galaxy tool ids": [ + "sonneityping" + ], + "Description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", + "bio.tool id": "sonneityping", + "bio.tool ids": [ + "sonneityping" + ], + "biii": null, + "bio.tool name": "sonneityping", + "bio.tool description": "Scripts for parsing Mykrobe predict results for Shigella sonnei.", + "EDAM operation": [ + "Antimicrobial resistance prediction", + "Variant calling", + "Genotyping" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Genotype and phenotype", + "Genetic variation", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/katholt/sonneityping", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "sonneityping", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/katholt/sonneityping", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping", + "Galaxy wrapper version": "20210201", + "Conda id": "sonneityping", + "Conda version": "20210201", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction", + "Variant calling", + "Genotyping" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Genotype and phenotype", + "Genetic variation", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spades", + "Galaxy tool ids": [ + "spades_biosyntheticspades", + "spades_coronaspades", + "spades_metaplasmidspades", + "metaspades", + "spades_metaviralspades", + "spades_plasmidspades", + "rnaspades", + "spades_rnaviralspades", + "spades" + ], + "Description": "SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.", + "bio.tool id": "spades", + "bio.tool ids": [ + "rnaviralspades", + "metaspades", + "spades", + "metaplasmidspades", + "plasmidspades", + "biosyntheticspades", + "coronaspades", + "rnaspades", + "metaviralspades" + ], + "biii": null, + "bio.tool name": "SPAdes", + "bio.tool description": "St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.", + "EDAM operation": [ + "Genome assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/ablab/spades", + "ToolShed categories": [ + "Assembly", + "RNA", + "Metagenomics" + ], + "ToolShed id": "spades", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades", + "Galaxy wrapper version": "3.15.5", + "Conda id": "spades", + "Conda version": "4.0.0", + "EDAM operation (no superclasses)": [ + "Genome assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 9, + "Available on UseGalaxy.org.au": 9, + "Available on UseGalaxy.eu": 9, + "Available on UseGalaxy.org.fr": 9 + }, + { + "Galaxy wrapper id": "spaln", + "Galaxy tool ids": [ + "list_spaln_tables", + "spaln" + ], + "Description": "Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/", + "ToolShed categories": [ + "Sequence Analysis", + "Genome annotation" + ], + "ToolShed id": "spaln", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/ogotoh/spaln", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln", + "Galaxy wrapper version": "2.4.9", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spotyping", + "Galaxy tool ids": [ + "spotyping" + ], + "Description": "SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads", + "bio.tool id": "spotyping", + "bio.tool ids": [ + "spotyping" + ], + "biii": null, + "bio.tool name": "SpoTyping", + "bio.tool description": "Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.", + "EDAM operation": [ + "Variant pattern analysis" + ], + "EDAM topic": [ + "Microbiology", + "Sequencing", + "Sequence composition, complexity and repeats", + "Genetic variation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/xiaeryu/SpoTyping-v2.0", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "spotyping", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping", + "Galaxy wrapper version": "2.1", + "Conda id": "spotyping", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [ + "Variant pattern analysis" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Sequencing", + "Sequence composition, complexity and repeats", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spyboat", + "Galaxy tool ids": [ + "spyboat" + ], + "Description": "Wavelet analysis for 3d-image stacks", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://github.com/tensionhead/spyboat", + "ToolShed categories": [ + "Imaging", + "Graphics" + ], + "ToolShed id": "spyboat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat", + "Galaxy wrapper version": "0.1.2", + "Conda id": "spyboat", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sra-tools", + "Galaxy tool ids": [ + "fasterq_dump", + "fastq_dump", + "sam_dump" + ], + "Description": "NCBI Sequence Read Archive toolkit utilities", + "bio.tool id": "sra-tools", + "bio.tool ids": [ + "sra-tools" + ], + "biii": null, + "bio.tool name": "SRA Software Toolkit", + "bio.tool description": "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.", + "EDAM operation": [ + "Data handling" + ], + "EDAM topic": [ + "DNA", + "Genomics", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "https://github.com/ncbi/sra-tools", + "ToolShed categories": [ + "Data Source", + "Fastq Manipulation" + ], + "ToolShed id": "sra_tools", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools", + "Galaxy wrapper version": "3.1.1", + "Conda id": "sra-tools", + "Conda version": "3.1.1", + "EDAM operation (no superclasses)": [ + "Data handling" + ], + "EDAM topic (no superclasses)": [ + "DNA", + "Genomics", + "Sequencing" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "srst2", + "Galaxy tool ids": [ + "srst2" + ], + "Description": "SRST2 Short Read Sequence Typing for Bacterial Pathogens", + "bio.tool id": "srst2", + "bio.tool ids": [ + "srst2" + ], + "biii": null, + "bio.tool name": "srst2", + "bio.tool description": "Short Read Sequence Typing for Bacterial Pathogens", + "EDAM operation": [ + "Multilocus sequence typing" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Public health and epidemiology" + ], + "Status": "To update", + "Source": "http://katholt.github.io/srst2/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "srst2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/katholt/srst2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2", + "Galaxy wrapper version": "0.2.0", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [ + "Multilocus sequence typing" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Public health and epidemiology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "stacks", + "Galaxy tool ids": [ + "stacks_assembleperead", + "stacks_clonefilter", + "stacks_cstacks", + "stacks_denovomap", + "stacks_genotypes", + "stacks_populations", + "stacks_procrad", + "stacks_pstacks", + "stacks_refmap", + "stacks_rxstacks", + "stacks_sstacks", + "stacks_stats", + "stacks_ustacks" + ], + "Description": "Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq", + "bio.tool id": "stacks", + "bio.tool ids": [ + "stacks" + ], + "biii": null, + "bio.tool name": "Stacks", + "bio.tool description": "Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.", + "EDAM operation": [ + "Data handling" + ], + "EDAM topic": [ + "Mapping", + "Population genetics" + ], + "Status": "To update", + "Source": "http://catchenlab.life.illinois.edu/stacks/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "stacks", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks", + "Galaxy wrapper version": null, + "Conda id": "stacks", + "Conda version": "2.65", + "EDAM operation (no superclasses)": [ + "Data handling" + ], + "EDAM topic (no superclasses)": [ + "Mapping", + "Population genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 13, + "Available on UseGalaxy.eu": 13, + "Available on UseGalaxy.org.fr": 12 + }, + { + "Galaxy wrapper id": "stacks2", + "Galaxy tool ids": [ + "stacks2_clonefilter", + "stacks2_cstacks", + "stacks2_denovomap", + "stacks2_gstacks", + "stacks2_kmerfilter", + "stacks2_populations", + "stacks2_procrad", + "stacks2_refmap", + "stacks2_shortreads", + "stacks2_sstacks", + "stacks2_tsv2bam", + "stacks2_ustacks" + ], + "Description": "Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://catchenlab.life.illinois.edu/stacks/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2", + "Galaxy wrapper version": "2.55", + "Conda id": "stacks", + "Conda version": "2.65", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 12, + "Available on UseGalaxy.eu": 12, + "Available on UseGalaxy.org.fr": 12 + }, + { + "Galaxy wrapper id": "star_fusion", + "Galaxy tool ids": [ + "star_fusion" + ], + "Description": "STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics" + ], + "ToolShed id": "star_fusion", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion", + "Galaxy wrapper version": "0.5.4-3+galaxy1", + "Conda id": "star-fusion", + "Conda version": "1.13.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "straindesign", + "Galaxy tool ids": [ + "straindesign_analyzing_model", + "straindesign_reduce_model", + "straindesign_simulate_deletion" + ], + "Description": "Toolbox to optimize biological model", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/brsynth/straindesign", + "ToolShed categories": [ + "Systems Biology", + "Synthetic Biology" + ], + "ToolShed id": "straindesign", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/brsynth/straindesign", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign", + "Galaxy wrapper version": "3.2.2", + "Conda id": "straindesign", + "Conda version": "3.2.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "strelka", + "Galaxy tool ids": [ + "strelka_germline", + "strelka_somatic" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/Illumina/strelka/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "strelka", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka", + "Galaxy wrapper version": "2.9.10", + "Conda id": "strelka", + "Conda version": "2.9.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "stringtie", + "Galaxy tool ids": [ + "stringtie", + "stringtie_merge" + ], + "Description": "StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.", + "bio.tool id": "stringtie", + "bio.tool ids": [ + "stringtie" + ], + "biii": null, + "bio.tool name": "StringTie", + "bio.tool description": "Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.", + "EDAM operation": [ + "Transcriptome assembly", + "RNA-Seq analysis" + ], + "EDAM topic": [ + "Transcriptomics", + "RNA-seq" + ], + "Status": "Up-to-date", + "Source": "http://ccb.jhu.edu/software/stringtie/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "stringtie", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie", + "Galaxy wrapper version": "2.2.3", + "Conda id": "stringtie", + "Conda version": "2.2.3", + "EDAM operation (no superclasses)": [ + "Transcriptome assembly", + "RNA-Seq analysis" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "structure", + "Galaxy tool ids": [ + "structure" + ], + "Description": "for using multi-locus genotype data to investigate population structure.", + "bio.tool id": "structure", + "bio.tool ids": [ + "structure" + ], + "biii": null, + "bio.tool name": "Structure", + "bio.tool description": "The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.", + "EDAM operation": [ + "Genetic variation analysis" + ], + "EDAM topic": [ + "Population genetics" + ], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Phylogenetics", + "Variant Analysis" + ], + "ToolShed id": "structure", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure", + "Galaxy wrapper version": "2.3.4", + "Conda id": "structure", + "Conda version": "2.3.4", + "EDAM operation (no superclasses)": [ + "Genetic variation analysis" + ], + "EDAM topic (no superclasses)": [ + "Population genetics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "structureharvester", + "Galaxy tool ids": [ + "structureharvester" + ], + "Description": "for parsing STRUCTURE outputs and for performing the Evanno method", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Phylogenetics", + "Variant Analysis" + ], + "ToolShed id": "structureharvester", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester", + "Galaxy wrapper version": "0.6.94", + "Conda id": "structureharvester", + "Conda version": "0.6.94", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "swift", + "Galaxy tool ids": [ + "swiftlink" + ], + "Description": "Parallel MCMC Linkage Analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/ajm/swiftlink", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "swiftlink", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift", + "Galaxy wrapper version": "1.0", + "Conda id": "swiftlink", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "syndiva", + "Galaxy tool ids": [ + "syndiva" + ], + "Description": "SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "syndiva", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva", + "Galaxy wrapper version": "1.0", + "Conda id": "clustalo", + "Conda version": "1.2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "table_compute", + "Galaxy tool ids": [ + "table_compute" + ], + "Description": "Perform general-purpose table operations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "table_compute", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute", + "Galaxy wrapper version": "1.2.4", + "Conda id": "pandas", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tag_pileup_frequency", + "Galaxy tool ids": [ + "tag_pileup_frequency" + ], + "Description": "Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup", + "ToolShed categories": [ + "Statistics", + "SAM", + "Genomic Interval Operations" + ], + "ToolShed id": "tag_pileup_frequency", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency", + "Galaxy wrapper version": "1.0.2", + "Conda id": "openjdk", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tasmanian_mismatch", + "Galaxy tool ids": [ + "tasmanian_mismatch" + ], + "Description": "Analysis of positional mismatches", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tasmanian_mismatch", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/nebiolabs/tasmanian-mismatch", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch", + "Galaxy wrapper version": "1.0.7", + "Conda id": "tasmanian-mismatch", + "Conda version": "1.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "taxonomy_filter_refseq", + "Galaxy tool ids": [ + "taxonomy_filter_refseq" + ], + "Description": "Filter RefSeq by taxonomy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/pvanheus/ncbitaxonomy", + "ToolShed categories": [ + "Sequence Analysis", + "Genome annotation" + ], + "ToolShed id": "taxonomy_filter_refseq", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq", + "Galaxy wrapper version": "0.3.0", + "Conda id": "rust-ncbitaxonomy", + "Conda version": "1.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "taxonomy_krona_chart", + "Galaxy tool ids": [ + "taxonomy_krona_chart" + ], + "Description": "Krona pie chart from taxonomic profile", + "bio.tool id": "krona", + "bio.tool ids": [ + "krona" + ], + "biii": null, + "bio.tool name": "Krona", + "bio.tool description": "Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).", + "EDAM operation": [ + "Visualisation" + ], + "EDAM topic": [ + "Metagenomics" + ], + "Status": "To update", + "Source": "http://sourceforge.net/projects/krona/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "taxonomy_krona_chart", + "Galaxy wrapper owner": "crs4", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart", + "Galaxy wrapper version": "2.7.1+galaxy0", + "Conda id": "krona", + "Conda version": "2.8.1", + "EDAM operation (no superclasses)": [ + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tb-profiler", + "Galaxy tool ids": [ + "tb_profiler_profile" + ], + "Description": "Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.", + "bio.tool id": "tb-profiler", + "bio.tool ids": [ + "tb-profiler" + ], + "biii": null, + "bio.tool name": "tb-profiler", + "bio.tool description": "A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).", + "EDAM operation": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/jodyphelan/TBProfiler", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tbprofiler", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler", + "Galaxy wrapper version": "6.2.1", + "Conda id": "tb-profiler", + "Conda version": "6.2.1", + "EDAM operation (no superclasses)": [ + "Antimicrobial resistance prediction" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tb_variant_filter", + "Galaxy tool ids": [ + "tb_variant_filter" + ], + "Description": "M. tuberculosis H37Rv VCF filter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/COMBAT-TB/tb_variant_filter", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "tb_variant_filter", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/COMBAT-TB/tb_variant_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter", + "Galaxy wrapper version": "0.4.0", + "Conda id": "tb_variant_filter", + "Conda version": "0.4.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tbl2gff3", + "Galaxy tool ids": [ + "tbl2gff3" + ], + "Description": "Table to GFF3", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3", + "ToolShed categories": [ + "Convert Formats", + "Sequence Analysis" + ], + "ToolShed id": "tbl2gff3", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3", + "Galaxy wrapper version": "1.2", + "Conda id": "bcbiogff", + "Conda version": "0.6.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tbvcfreport", + "Galaxy tool ids": [ + "tbvcfreport" + ], + "Description": "Generate HTML report from SnpEff M.tuberculosis VCF(s)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/COMBAT-TB/tbvcfreport", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "tbvcfreport", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport", + "Galaxy wrapper version": "1.0.0", + "Conda id": "tbvcfreport", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "te_finder", + "Galaxy tool ids": [ + "te_finder" + ], + "Description": "Transposable element insertions finder", + "bio.tool id": "tefinder", + "bio.tool ids": [ + "tefinder" + ], + "biii": null, + "bio.tool name": "TEfinder", + "bio.tool description": "A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.", + "EDAM operation": [ + "Genome indexing", + "Variant calling", + "PCR primer design" + ], + "EDAM topic": [ + "Sequencing", + "Mobile genetic elements", + "Workflows", + "Evolutionary biology", + "Genetic variation" + ], + "Status": "To update", + "Source": "https://github.com/VistaSohrab/TEfinder", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "te_finder", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder", + "Galaxy wrapper version": "1.0.1", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [ + "Genome indexing", + "Variant calling", + "PCR primer design" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Mobile genetic elements", + "Workflows", + "Evolutionary biology", + "Genetic variation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "telescope", + "Galaxy tool ids": [ + "telescope_assign" + ], + "Description": "Single locus resolution of Transposable ELEment expression.", + "bio.tool id": "Telescope-expression", + "bio.tool ids": [ + "Telescope-expression" + ], + "biii": null, + "bio.tool name": "Telescope", + "bio.tool description": "Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.", + "EDAM operation": [ + "Essential dynamics", + "Sequence trimming", + "RNA-Seq quantification", + "Expression analysis", + "Read mapping" + ], + "EDAM topic": [ + "RNA-Seq", + "Transcriptomics", + "Mapping", + "Gene transcripts", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/mlbendall/telescope/", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "telescope_assign", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope", + "Galaxy wrapper version": "1.0.3", + "Conda id": "telescope", + "Conda version": "1.0.3", + "EDAM operation (no superclasses)": [ + "Essential dynamics", + "Sequence trimming", + "RNA-Seq quantification", + "Expression analysis", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "RNA-Seq", + "Transcriptomics", + "Mapping", + "Gene transcripts", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tetoolkit", + "Galaxy tool ids": [ + "tetoolkit_tetranscripts" + ], + "Description": "The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hammelllab.labsites.cshl.edu/software/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tetoolkit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/mhammell-laboratory/TEtranscripts", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit", + "Galaxy wrapper version": "2.2.3", + "Conda id": "tetranscripts", + "Conda version": "2.2.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tetyper", + "Galaxy tool ids": [ + "tetyper" + ], + "Description": "Type a specific transposable element (TE) of interest from paired-end sequencing data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/aesheppard/TETyper", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tetyper", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper", + "Galaxy wrapper version": "1.1", + "Conda id": "tetyper", + "Conda version": "1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tn93", + "Galaxy tool ids": [ + "tn93_readreduce", + "tn93", + "tn93_cluster", + "tn93_filter" + ], + "Description": "Compute distances between sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/veg/tn93/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tn93", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93", + "Galaxy wrapper version": "1.0.6", + "Conda id": "tn93", + "Conda version": "1.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tooldistillator", + "Galaxy tool ids": [ + "tooldistillator", + "tooldistillator_summarize" + ], + "Description": "ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files", + "bio.tool id": "tooldistillator", + "bio.tool ids": [ + "tooldistillator" + ], + "biii": null, + "bio.tool name": "ToolDistillator", + "bio.tool description": "ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.", + "EDAM operation": [ + "Data handling", + "Parsing" + ], + "EDAM topic": [ + "Microbiology", + "Bioinformatics", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://gitlab.com/ifb-elixirfr/abromics/tooldistillator", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "tooldistillator", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator", + "Galaxy wrapper version": "0.8.5.0", + "Conda id": "tooldistillator", + "Conda version": "0.8.5.0", + "EDAM operation (no superclasses)": [ + "Parsing" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Bioinformatics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "tracegroomer", + "Galaxy tool ids": [ + "tracegroomer" + ], + "Description": "TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/cbib/TraceGroomer", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer", + "Galaxy wrapper version": "0.1.3", + "Conda id": "tracegroomer", + "Conda version": "0.1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tracy", + "Galaxy tool ids": [ + "tracy_align", + "tracy_assemble", + "tracy_basecall", + "tracy_decompose" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy", + "Galaxy wrapper version": "0.6.1", + "Conda id": "tracy", + "Conda version": "0.7.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "transdecoder", + "Galaxy tool ids": [ + "transdecoder" + ], + "Description": "TransDecoder finds coding regions within transcripts", + "bio.tool id": "TransDecoder", + "bio.tool ids": [ + "TransDecoder" + ], + "biii": null, + "bio.tool name": "TransDecoder", + "bio.tool description": "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.", + "EDAM operation": [ + "Coding region prediction", + "de Novo sequencing", + "De-novo assembly" + ], + "EDAM topic": [ + "Genomics", + "Gene transcripts", + "RNA-Seq", + "Gene expression", + "Sequence assembly", + "Whole genome sequencing" + ], + "Status": "To update", + "Source": "https://transdecoder.github.io/", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": "transdecoder", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder", + "Galaxy wrapper version": "5.5.0", + "Conda id": "transdecoder", + "Conda version": "5.7.1", + "EDAM operation (no superclasses)": [ + "Coding region prediction", + "de Novo sequencing", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Gene transcripts", + "RNA-Seq", + "Gene expression", + "Sequence assembly", + "Whole genome sequencing" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "transit", + "Galaxy tool ids": [ + "gff_to_prot", + "transit_gumbel", + "transit_hmm", + "transit_resampling", + "transit_tn5gaps" + ], + "Description": "TRANSIT", + "bio.tool id": "transit", + "bio.tool ids": [ + "transit" + ], + "biii": null, + "bio.tool name": "TRANSIT", + "bio.tool description": "A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.", + "EDAM operation": [ + "Transposon prediction" + ], + "EDAM topic": [ + "DNA", + "Sequencing", + "Mobile genetic elements" + ], + "Status": "To update", + "Source": "https://github.com/mad-lab/transit/", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit", + "Galaxy wrapper version": "3.0.2", + "Conda id": "transit", + "Conda version": "3.2.3", + "EDAM operation (no superclasses)": [ + "Transposon prediction" + ], + "EDAM topic (no superclasses)": [ + "DNA", + "Sequencing", + "Mobile genetic elements" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "transtermhp", + "Galaxy tool ids": [ + "transtermhp" + ], + "Description": "Finds rho-independent transcription terminators in bacterial genomes", + "bio.tool id": "transtermhp", + "bio.tool ids": [ + "transtermhp" + ], + "biii": null, + "bio.tool name": "TransTermHP", + "bio.tool description": "TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator", + "EDAM operation": [ + "Transcriptional regulatory element prediction" + ], + "EDAM topic": [ + "Transcription factors and regulatory sites" + ], + "Status": "To update", + "Source": "https://transterm.cbcb.umd.edu", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "transtermhp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp", + "Galaxy wrapper version": null, + "Conda id": "transtermhp", + "Conda version": "2.09", + "EDAM operation (no superclasses)": [ + "Transcriptional regulatory element prediction" + ], + "EDAM topic (no superclasses)": [ + "Transcription factors and regulatory sites" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "trimmomatic", + "Galaxy tool ids": [ + "trimmomatic" + ], + "Description": "A flexible read trimming tool for Illumina NGS data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://www.usadellab.org/cms/?page=trimmomatic", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "trimmomatic", + "Galaxy wrapper owner": "pjbriggs", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic", + "Galaxy wrapper version": "0.39", + "Conda id": "trimmomatic", + "Conda version": "0.39", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "trinity", + "Galaxy tool ids": [ + "trinity_abundance_estimates_to_matrix", + "trinity_align_and_estimate_abundance", + "trinity_analyze_diff_expr", + "trinity_contig_exn50_statistic", + "trinity_define_clusters_by_cutting_tree", + "describe_samples", + "trinity_filter_low_expr_transcripts", + "trinity_gene_to_trans_map", + "trinity_run_de_analysis", + "trinity_samples_qccheck", + "trinity_super_transcripts", + "trinity", + "trinity_stats" + ], + "Description": "Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq", + "bio.tool id": "trinity", + "bio.tool ids": [ + "trinity" + ], + "biii": null, + "bio.tool name": "Trinity", + "bio.tool description": "Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.", + "EDAM operation": [ + "Transcriptome assembly" + ], + "EDAM topic": [ + "Transcriptomics", + "Gene expression", + "Gene transcripts" + ], + "Status": "Up-to-date", + "Source": "https://github.com/trinityrnaseq/trinityrnaseq", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity", + "Galaxy wrapper version": "2.15.1", + "Conda id": "trinity", + "Conda version": "2.15.1", + "EDAM operation (no superclasses)": [ + "Transcriptome assembly" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Gene transcripts" + ], + "Available on UseGalaxy.org": 9, + "Available on UseGalaxy.org.au": 13, + "Available on UseGalaxy.eu": 13, + "Available on UseGalaxy.org.fr": 13 + }, + { + "Galaxy wrapper id": "trinotate", + "Galaxy tool ids": [ + "trinotate" + ], + "Description": "Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.", + "bio.tool id": "trinotate", + "bio.tool ids": [ + "trinotate" + ], + "biii": null, + "bio.tool name": "Trinotate", + "bio.tool description": "Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.", + "EDAM operation": [ + "Gene functional annotation" + ], + "EDAM topic": [ + "Gene expression", + "Transcriptomics" + ], + "Status": "To update", + "Source": "https://trinotate.github.io/", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": "trinotate", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate", + "Galaxy wrapper version": "3.2.2", + "Conda id": "trinotate", + "Conda version": "4.0.2", + "EDAM operation (no superclasses)": [ + "Gene functional annotation" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "trycycler", + "Galaxy tool ids": [ + "trycycler_cluster", + "trycycler_consensus", + "trycycler_partition", + "trycycler_reconcile_msa", + "trycycler_subsample" + ], + "Description": "Trycycler toolkit wrappers", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/rrwick/Trycycler", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "trycycler", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler", + "Galaxy wrapper version": "0.5.5", + "Conda id": "trycycler", + "Conda version": "0.5.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "tsebra", + "Galaxy tool ids": [ + "tsebra" + ], + "Description": "This tool has been developed to combine BRAKER predictions.", + "bio.tool id": "tsebra", + "bio.tool ids": [ + "tsebra" + ], + "biii": null, + "bio.tool name": "TSEBRA", + "bio.tool description": "TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.", + "EDAM operation": [ + "Homology-based gene prediction", + "Alternative splicing prediction" + ], + "EDAM topic": [ + "Gene expression", + "RNA-Seq", + "Gene transcripts", + "Model organisms" + ], + "Status": "To update", + "Source": "https://github.com/Gaius-Augustus/TSEBRA", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra", + "Galaxy wrapper version": "1.1.2.4", + "Conda id": "tsebra", + "Conda version": "1.1.2.5", + "EDAM operation (no superclasses)": [ + "Homology-based gene prediction", + "Alternative splicing prediction" + ], + "EDAM topic (no superclasses)": [ + "Gene expression", + "RNA-Seq", + "Gene transcripts", + "Model organisms" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tsne", + "Galaxy tool ids": [ + "tsne" + ], + "Description": "T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cran.r-project.org/web/packages/Rtsne/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "tsne", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne", + "Galaxy wrapper version": "0.0.2", + "Conda id": "r-rtsne", + "Conda version": "0.13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "tximport", + "Galaxy tool ids": [ + "tximport" + ], + "Description": "Wrapper for the Bioconductor package tximport", + "bio.tool id": "tximport", + "bio.tool ids": [ + "tximport" + ], + "biii": null, + "bio.tool name": "tximport", + "bio.tool description": "An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.", + "EDAM operation": [ + "Pathway or network analysis", + "Formatting", + "RNA-Seq analysis" + ], + "EDAM topic": [ + "Transcriptomics", + "Gene transcripts", + "Workflows" + ], + "Status": "To update", + "Source": "http://bioconductor.org/packages/tximport/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "tximport", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport", + "Galaxy wrapper version": "1.22.0", + "Conda id": "bioconductor-tximport", + "Conda version": "1.30.0", + "EDAM operation (no superclasses)": [ + "Pathway or network analysis", + "Formatting", + "RNA-Seq analysis" + ], + "EDAM topic (no superclasses)": [ + "Transcriptomics", + "Gene transcripts", + "Workflows" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ucsc_blat", + "Galaxy tool ids": [ + "ucsc_blat" + ], + "Description": "Standalone blat sequence search command line tool", + "bio.tool id": "blat", + "bio.tool ids": [ + "blat" + ], + "biii": null, + "bio.tool name": "BLAT", + "bio.tool description": "Fast, accurate spliced alignment of DNA sequences.", + "EDAM operation": [ + "Sequence alignment" + ], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "http://genome.ucsc.edu/goldenPath/help/blatSpec.html", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ucsc_blat", + "Galaxy wrapper owner": "yating-l", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat", + "Galaxy wrapper version": "377", + "Conda id": "ucsc-blat", + "Conda version": "445", + "EDAM operation (no superclasses)": [ + "Sequence alignment" + ], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasplit", + "Galaxy tool ids": [ + "fasplit" + ], + "Description": "faSplit is a tool to split a single FASTA file into several files", + "bio.tool id": "UCSC_Genome_Browser_Utilities", + "bio.tool ids": [ + "UCSC_Genome_Browser_Utilities" + ], + "biii": null, + "bio.tool name": "UCSC Genome Browser Utilities", + "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "ucsc_fasplit", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit", + "Galaxy wrapper version": "377", + "Conda id": "ucsc-fasplit", + "Conda version": "377", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fatovcf", + "Galaxy tool ids": [ + "fatovcf" + ], + "Description": "Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs", + "bio.tool id": "UCSC_Genome_Browser_Utilities", + "bio.tool ids": [ + "UCSC_Genome_Browser_Utilities" + ], + "biii": null, + "bio.tool name": "UCSC Genome Browser Utilities", + "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "ucsc_fatovcf", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf", + "Galaxy wrapper version": "448", + "Conda id": "ucsc-fatovcf", + "Conda version": "448", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "twobittofa", + "Galaxy tool ids": [ + "ucsc-twobittofa" + ], + "Description": "twoBitToFa is a tool to convert all or part of .2bit file to FASTA", + "bio.tool id": "UCSC_Genome_Browser_Utilities", + "bio.tool ids": [ + "UCSC_Genome_Browser_Utilities" + ], + "biii": null, + "bio.tool name": "UCSC Genome Browser Utilities", + "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://genome.ucsc.edu/goldenpath/help/twoBit.html", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "ucsc_twobittofa", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa", + "Galaxy wrapper version": "377", + "Conda id": "ucsc-twobittofa", + "Conda version": "455", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "wigtobigwig", + "Galaxy tool ids": [ + "ucsc_wigtobigwig" + ], + "Description": "converts bedGraph (wig) files into binary bigwig", + "bio.tool id": "UCSC_Genome_Browser_Utilities", + "bio.tool ids": [ + "UCSC_Genome_Browser_Utilities" + ], + "biii": null, + "bio.tool name": "UCSC Genome Browser Utilities", + "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.", + "EDAM operation": [], + "EDAM topic": [ + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://genome.ucsc.edu/goldenPath/help/bigWig.html", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "ucsc_wigtobigwig", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig", + "Galaxy wrapper version": "447", + "Conda id": "ucsc-wigtobigwig", + "Conda version": "447", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [ + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "umi_tools", + "Galaxy tool ids": [ + "umi_tools_count", + "umi_tools_dedup", + "umi_tools_extract", + "umi_tools_group", + "umi_tools_whitelist" + ], + "Description": "UMI-tools extract - Extract UMIs from fastq", + "bio.tool id": "umi-tools", + "bio.tool ids": [ + "umi-tools" + ], + "biii": null, + "bio.tool name": "UMI-tools", + "bio.tool description": "Tools for handling Unique Molecular Identifiers in NGS data sets.", + "EDAM operation": [ + "Sequencing quality control" + ], + "EDAM topic": [ + "NGS", + "Sequence sites, features and motifs", + "Quality affairs" + ], + "Status": "To update", + "Source": "https://github.com/CGATOxford/UMI-tools", + "ToolShed categories": [ + "Sequence Analysis", + "Transcriptomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools", + "Galaxy wrapper version": "1.1.2", + "Conda id": "umi_tools", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [ + "Sequencing quality control" + ], + "EDAM topic (no superclasses)": [ + "Sequence sites, features and motifs", + "Quality affairs" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "unicycler", + "Galaxy tool ids": [ + "unicycler" + ], + "Description": "Unicycler is a hybrid assembly pipeline for bacterial genomes.", + "bio.tool id": "unicycler", + "bio.tool ids": [ + "unicycler" + ], + "biii": null, + "bio.tool name": "Unicycler", + "bio.tool description": "A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.", + "EDAM operation": [ + "Genome assembly", + "Aggregation" + ], + "EDAM topic": [ + "Microbiology", + "Genomics", + "Sequencing", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/rrwick/Unicycler", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "unicycler", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler", + "Galaxy wrapper version": "0.5.0", + "Conda id": "unicycler", + "Conda version": "0.5.0", + "EDAM operation (no superclasses)": [ + "Genome assembly", + "Aggregation" + ], + "EDAM topic (no superclasses)": [ + "Microbiology", + "Genomics", + "Sequencing", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "usher", + "Galaxy tool ids": [ + "usher_matutils", + "usher" + ], + "Description": "UShER toolkit wrappers", + "bio.tool id": "usher", + "bio.tool ids": [ + "usher" + ], + "biii": null, + "bio.tool name": "usher", + "bio.tool description": "The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.", + "EDAM operation": [ + "Classification", + "Phylogenetic tree visualisation", + "Phylogenetic inference (from molecular sequences)" + ], + "EDAM topic": [ + "Phylogeny", + "Evolutionary biology", + "Cladistics", + "Genotype and phenotype", + "Phylogenomics" + ], + "Status": "To update", + "Source": "https://github.com/yatisht/usher", + "ToolShed categories": [ + "Phylogenetics" + ], + "ToolShed id": "usher", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher", + "Galaxy wrapper version": "0.2.1", + "Conda id": "usher", + "Conda version": "0.6.3", + "EDAM operation (no superclasses)": [ + "Classification", + "Phylogenetic tree visualisation", + "Phylogenetic inference (from molecular sequences)" + ], + "EDAM topic (no superclasses)": [ + "Cladistics", + "Genotype and phenotype", + "Phylogenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "valet", + "Galaxy tool ids": [ + "valet" + ], + "Description": "A pipeline for detecting mis-assemblies in metagenomic assemblies.", + "bio.tool id": "valet", + "bio.tool ids": [ + "valet" + ], + "biii": null, + "bio.tool name": "VALET", + "bio.tool description": "VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.", + "EDAM operation": [ + "Sequence assembly", + "Sequence assembly visualisation" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://github.com/marbl/VALET", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "valet", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet", + "Galaxy wrapper version": null, + "Conda id": "valet", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [ + "Sequence assembly", + "Sequence assembly visualisation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vapor", + "Galaxy tool ids": [ + "vapor" + ], + "Description": "Classify Influenza samples from raw short read sequence data", + "bio.tool id": "vapor", + "bio.tool ids": [ + "vapor" + ], + "biii": null, + "bio.tool name": "VAPOR", + "bio.tool description": "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.", + "EDAM operation": [ + "Data retrieval", + "De-novo assembly", + "Read mapping" + ], + "EDAM topic": [ + "Whole genome sequencing", + "Mapping", + "Sequence assembly" + ], + "Status": "Up-to-date", + "Source": "https://github.com/connor-lab/vapor", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "vapor", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor", + "Galaxy wrapper version": "1.0.2", + "Conda id": "vapor", + "Conda version": "1.0.2", + "EDAM operation (no superclasses)": [ + "Data retrieval", + "De-novo assembly", + "Read mapping" + ], + "EDAM topic (no superclasses)": [ + "Whole genome sequencing", + "Mapping", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vardict", + "Galaxy tool ids": [ + "vardict_java" + ], + "Description": "VarDict - calls SNVs and indels for tumour-normal pairs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AstraZeneca-NGS/VarDictJava", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vardict_java", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict", + "Galaxy wrapper version": "1.8.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "variant_analyzer", + "Galaxy tool ids": [ + "mut2read", + "mut2sscs", + "read2mut" + ], + "Description": "Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "variant_analyzer", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer", + "Galaxy wrapper version": "2.0.0", + "Conda id": "matplotlib", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "varscan", + "Galaxy tool ids": [ + "varscan_copynumber", + "varscan_mpileup", + "varscan_somatic" + ], + "Description": "VarScan is a variant caller for high-throughput sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://dkoboldt.github.io/varscan/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "varscan", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/iuc/tree/master/tools/varscan", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan", + "Galaxy wrapper version": "2.4.3", + "Conda id": "varscan", + "Conda version": "2.4.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "varvamp", + "Galaxy tool ids": [ + "varvamp" + ], + "Description": "Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses", + "bio.tool id": "varvamp", + "bio.tool ids": [ + "varvamp" + ], + "biii": null, + "bio.tool name": "varVAMP", + "bio.tool description": "variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.", + "EDAM operation": [ + "PCR primer design" + ], + "EDAM topic": [ + "Virology" + ], + "Status": "Up-to-date", + "Source": "https://github.com/jonas-fuchs/varVAMP/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "varvamp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/jonas-fuchs/varVAMP", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp", + "Galaxy wrapper version": "1.2.0", + "Conda id": "varvamp", + "Conda version": "1.2.0", + "EDAM operation (no superclasses)": [ + "PCR primer design" + ], + "EDAM topic (no superclasses)": [ + "Virology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vcf2maf", + "Galaxy tool ids": [ + "vcf2maf" + ], + "Description": "vcf2maf: Convert VCF into MAF", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "vcf2maf", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf", + "Galaxy wrapper version": "1.6.21", + "Conda id": "vcf2maf", + "Conda version": "1.6.22", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vcfanno", + "Galaxy tool ids": [ + "vcfanno" + ], + "Description": "Annotate VCF files", + "bio.tool id": "vcfanno", + "bio.tool ids": [ + "vcfanno" + ], + "biii": null, + "bio.tool name": "vcfanno", + "bio.tool description": "Fast, flexible annotation of genetic variants.", + "EDAM operation": [ + "SNP annotation" + ], + "EDAM topic": [ + "Genetic variation", + "Data submission, annotation and curation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/brentp/vcfanno", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfanno", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/vcfanno/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno", + "Galaxy wrapper version": "0.3.5", + "Conda id": "vcfanno", + "Conda version": "0.3.5", + "EDAM operation (no superclasses)": [ + "SNP annotation" + ], + "EDAM topic (no superclasses)": [ + "Genetic variation", + "Data submission, annotation and curation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vegan", + "Galaxy tool ids": [ + "vegan_diversity", + "vegan_fisher_alpha", + "vegan_rarefaction" + ], + "Description": "an R package fo community ecologist", + "bio.tool id": "vegan", + "bio.tool ids": [ + "vegan" + ], + "biii": null, + "bio.tool name": "vegan", + "bio.tool description": "Ordination methods, diversity analysis and other functions for community and vegetation ecologists", + "EDAM operation": [ + "Standardisation and normalisation", + "Analysis" + ], + "EDAM topic": [ + "Ecology", + "Phylogenetics", + "Environmental science" + ], + "Status": "To update", + "Source": "https://cran.r-project.org/package=vegan", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan", + "Galaxy wrapper version": "2.4-3", + "Conda id": "r-vegan", + "Conda version": "2.3_4", + "EDAM operation (no superclasses)": [ + "Standardisation and normalisation", + "Analysis" + ], + "EDAM topic (no superclasses)": [ + "Ecology", + "Phylogenetics", + "Environmental science" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "velocyto", + "Galaxy tool ids": [ + "velocyto_cli" + ], + "Description": "Velocyto is a library for the analysis of RNA velocity.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://velocyto.org/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "velocyto", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto", + "Galaxy wrapper version": "0.17.17", + "Conda id": "velocyto.py", + "Conda version": "0.17.17", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "velvet", + "Galaxy tool ids": [ + "velvetg", + "velveth" + ], + "Description": "de novo genomic assembler specially designed for short read sequencing technologies", + "bio.tool id": "velvet", + "bio.tool ids": [ + "velvet" + ], + "biii": null, + "bio.tool name": "Velvet", + "bio.tool description": "A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.", + "EDAM operation": [ + "Formatting", + "De-novo assembly" + ], + "EDAM topic": [ + "Sequence assembly" + ], + "Status": "To update", + "Source": "https://www.ebi.ac.uk/~zerbino/velvet/", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "velvet", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet", + "Galaxy wrapper version": null, + "Conda id": "velvet", + "Conda version": "1.2.10", + "EDAM operation (no superclasses)": [ + "Formatting", + "De-novo assembly" + ], + "EDAM topic (no superclasses)": [ + "Sequence assembly" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "velvet_optimiser", + "Galaxy tool ids": [ + "velvetoptimiser" + ], + "Description": "Automatically optimize Velvet assemblies", + "bio.tool id": "velvetoptimiser", + "bio.tool ids": [ + "velvetoptimiser" + ], + "biii": null, + "bio.tool name": "VelvetOptimiser", + "bio.tool description": "This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.", + "EDAM operation": [ + "Optimisation and refinement", + "Sequence assembly" + ], + "EDAM topic": [ + "Genomics", + "Sequence assembly" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "velvetoptimiser", + "Galaxy wrapper owner": "simon-gladman", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser", + "Galaxy wrapper version": "2.2.6+galaxy2", + "Conda id": "velvet", + "Conda version": "1.2.10", + "EDAM operation (no superclasses)": [ + "Optimisation and refinement", + "Sequence assembly" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Sequence assembly" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "verkko", + "Galaxy tool ids": [ + "verkko" + ], + "Description": "Telomere-to-telomere assembly pipeline", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/marbl/verkko", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "verkko", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko", + "Galaxy wrapper version": "1.3.1", + "Conda id": "verkko", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vg", + "Galaxy tool ids": [ + "vg_convert", + "vg_deconstruct", + "vg_view" + ], + "Description": "Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/vgteam/vg", + "ToolShed categories": [ + "Sequence Analysis", + "Variant Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg", + "Galaxy wrapper version": "1.23.0", + "Conda id": "vg", + "Conda version": "1.56.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "virAnnot", + "Galaxy tool ids": [ + "virannot_blast2tsv", + "virannot_otu", + "virAnnot_rps2tsv" + ], + "Description": "virAnnot wrappers", + "bio.tool id": "virannot", + "bio.tool ids": [ + "virannot" + ], + "biii": null, + "bio.tool name": "virAnnot", + "bio.tool description": "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project \"Plant Health Bioinformatics Network\". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.", + "EDAM operation": [ + "Sequence annotation", + "Sequence clustering", + "Sequence cluster visualisation" + ], + "EDAM topic": [ + "Metagenomics", + "Virology", + "Microbial ecology" + ], + "Status": "To update", + "Source": "https://github.com/marieBvr/virAnnot", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "virannot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot", + "Galaxy wrapper version": "1.0.0+galaxy0", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [ + "Sequence annotation", + "Sequence clustering", + "Sequence cluster visualisation" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Virology", + "Microbial ecology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "virheat", + "Galaxy tool ids": [ + "virheat" + ], + "Description": "generates a heatmap of allele frequencies from vcf files", + "bio.tool id": "virheat", + "bio.tool ids": [ + "virheat" + ], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/jonas-fuchs/virHEAT", + "ToolShed categories": [ + "Visualization", + "Variant Analysis" + ], + "ToolShed id": "virheat", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat", + "Galaxy wrapper version": "0.7", + "Conda id": "virheat", + "Conda version": "0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "virhunter", + "Galaxy tool ids": [ + "virhunter" + ], + "Description": "Deep Learning method for novel virus detection in sequencing data", + "bio.tool id": "virhunter", + "bio.tool ids": [ + "virhunter" + ], + "biii": null, + "bio.tool name": "VirHunter", + "bio.tool description": "VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).", + "EDAM operation": [ + "Sequence classification" + ], + "EDAM topic": [ + "Virology" + ], + "Status": "To update", + "Source": "https://github.com/cbib/virhunter", + "ToolShed categories": [ + "Machine Learning" + ], + "ToolShed id": "virhunter", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter", + "Galaxy wrapper version": "1.0.0", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Sequence classification" + ], + "EDAM topic (no superclasses)": [ + "Virology" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "volcanoplot", + "Galaxy tool ids": [ + "volcanoplot" + ], + "Description": "Tool to create a Volcano Plot", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://ggplot2.tidyverse.org/", + "ToolShed categories": [ + "Visualization", + "Transcriptomics", + "Statistics" + ], + "ToolShed id": "volcanoplot", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot", + "Galaxy wrapper version": "0.0.6", + "Conda id": "r-ggplot2", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vsearch", + "Galaxy tool ids": [ + "vsearch_alignment", + "vsearch_chimera_detection", + "vsearch_clustering", + "vsearch_dereplication", + "vsearch_masking", + "vsearch_search", + "vsearch_shuffling", + "vsearch_sorting" + ], + "Description": "VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.", + "bio.tool id": "vsearch", + "bio.tool ids": [ + "vsearch" + ], + "biii": null, + "bio.tool name": "VSEARCH", + "bio.tool description": "High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.", + "EDAM operation": [ + "DNA mapping", + "Chimera detection" + ], + "EDAM topic": [ + "Metagenomics", + "Sequence analysis" + ], + "Status": "To update", + "Source": "https://github.com/torognes/vsearch", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "vsearch", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch", + "Galaxy wrapper version": "2.8.3", + "Conda id": "vsearch", + "Conda version": "2.28.1", + "EDAM operation (no superclasses)": [ + "DNA mapping", + "Chimera detection" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 8, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 8 + }, + { + "Galaxy wrapper id": "vsnp", + "Galaxy tool ids": [ + "vsnp_add_zero_coverage", + "vsnp_build_tables", + "vsnp_determine_ref_from_data", + "vsnp_get_snps", + "vsnp_statistics" + ], + "Description": "The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/USDA-VS/vSNP", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "vsnp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp", + "Galaxy wrapper version": "3.0.6", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "weather_app", + "Galaxy tool ids": [ + "simple_weather" + ], + "Description": "provides simple weather in text format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://wttr.in/", + "ToolShed categories": [ + "Visualization", + "Web Services" + ], + "ToolShed id": "simpleweather", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app", + "Galaxy wrapper version": "0.1.2", + "Conda id": "curl", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "weblogo3", + "Galaxy tool ids": [ + "rgweblogo3" + ], + "Description": "Sequence Logo generator for fasta", + "bio.tool id": "weblogo", + "bio.tool ids": [ + "weblogo" + ], + "biii": null, + "bio.tool name": "WebLogo", + "bio.tool description": "Web-based application designed to make generate sequence logos.", + "EDAM operation": [ + "Sequence cluster visualisation", + "Sequence visualisation", + "Sequence motif recognition" + ], + "EDAM topic": [ + "Nucleic acid sites, features and motifs", + "Sequence analysis" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Graphics" + ], + "ToolShed id": "weblogo3", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3", + "Galaxy wrapper version": "3.5.0", + "Conda id": "weblogo", + "Conda version": "3.7.9", + "EDAM operation (no superclasses)": [ + "Sequence cluster visualisation", + "Sequence visualisation", + "Sequence motif recognition" + ], + "EDAM topic (no superclasses)": [ + "Nucleic acid sites, features and motifs", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "windowmasker", + "Galaxy tool ids": [ + "windowmasker_mkcounts", + "windowmasker_ustat" + ], + "Description": "Identify repetitive regions using WindowMasker", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "windowmasker", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker", + "Galaxy wrapper version": "1.0", + "Conda id": "blast", + "Conda version": "2.15.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "winnowmap", + "Galaxy tool ids": [ + "winnowmap" + ], + "Description": "A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/marbl/Winnowmap", + "ToolShed categories": [ + "Next Gen Mappers" + ], + "ToolShed id": "winnowmap", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap", + "Galaxy wrapper version": "2.03", + "Conda id": "winnowmap", + "Conda version": "2.03", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "xpath", + "Galaxy tool ids": [ + "xpath" + ], + "Description": "XPath XML querying tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://search.cpan.org/dist/XML-XPath/", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "xpath", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath", + "Galaxy wrapper version": null, + "Conda id": "perl-xml-xpath", + "Conda version": "1.47", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "yahs", + "Galaxy tool ids": [ + "yahs" + ], + "Description": "Yet Another Hi-C scaffolding tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/c-zhou/yahs", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "yahs", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs", + "Galaxy wrapper version": "1.2a.2", + "Conda id": "yahs", + "Conda version": "1.2a.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "zerone", + "Galaxy tool ids": [ + "zerone" + ], + "Description": "ChIP-seq discretization and quality control", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/nanakiksc/zerone", + "ToolShed categories": [ + "ChIP-seq" + ], + "ToolShed id": "zerone", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone", + "Galaxy wrapper version": "1.0", + "Conda id": "zerone", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bamtools", + "Galaxy tool ids": [ + "bamtools" + ], + "Description": "Operate on and transform BAM datasets in various ways using bamtools", + "bio.tool id": "bamtools", + "bio.tool ids": [ + "bamtools" + ], + "biii": null, + "bio.tool name": "BamTools", + "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", + "EDAM operation": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic": [ + "Sequencing", + "Data management", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pezmaster31/bamtools", + "ToolShed categories": [ + "Sequence Analysis", + "SAM" + ], + "ToolShed id": "bamtools", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools", + "Galaxy wrapper version": "2.5.2", + "Conda id": "bamtools", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bamtools_filter", + "Galaxy tool ids": [ + "bamFilter" + ], + "Description": "Filter BAM datasets on various attributes using bamtools filter", + "bio.tool id": "bamtools", + "bio.tool ids": [ + "bamtools" + ], + "biii": null, + "bio.tool name": "BamTools", + "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", + "EDAM operation": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic": [ + "Sequencing", + "Data management", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pezmaster31/bamtools", + "ToolShed categories": [ + "Sequence Analysis", + "SAM" + ], + "ToolShed id": "bamtools_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter", + "Galaxy wrapper version": "2.5.2", + "Conda id": "bamtools", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "bamtools_split", + "Galaxy tool ids": [ + "bamtools_split_mapped", + "bamtools_split_paired", + "bamtools_split_ref", + "bamtools_split_tag" + ], + "Description": "Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.", + "bio.tool id": "bamtools", + "bio.tool ids": [ + "bamtools" + ], + "biii": null, + "bio.tool name": "BamTools", + "bio.tool description": "BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.", + "EDAM operation": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic": [ + "Sequencing", + "Data management", + "Sequence analysis" + ], + "Status": "Up-to-date", + "Source": "https://github.com/pezmaster31/bamtools", + "ToolShed categories": [ + "Sequence Analysis", + "SAM" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split", + "Galaxy wrapper version": "2.5.2", + "Conda id": "bamtools", + "Conda version": "2.5.2", + "EDAM operation (no superclasses)": [ + "Data handling", + "Sequence alignment analysis" + ], + "EDAM topic (no superclasses)": [ + "Sequencing", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "biotradis", + "Galaxy tool ids": [ + "bacteria_tradis", + "tradis_essentiality", + "tradis_gene_insert_sites" + ], + "Description": "Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.", + "bio.tool id": "biotradis", + "bio.tool ids": [ + "biotradis" + ], + "biii": null, + "bio.tool name": "biotradis", + "bio.tool description": "The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.", + "EDAM operation": [ + "Sequence analysis" + ], + "EDAM topic": [ + "Mobile genetic elements", + "Workflows" + ], + "Status": "Up-to-date", + "Source": "https://www.sanger.ac.uk/science/tools/bio-tradis", + "ToolShed categories": [ + "Genome annotation" + ], + "ToolShed id": "biotradis", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis", + "Galaxy wrapper version": "1.4.5", + "Conda id": "biotradis", + "Conda version": "1.4.5", + "EDAM operation (no superclasses)": [ + "Sequence analysis" + ], + "EDAM topic (no superclasses)": [ + "Mobile genetic elements", + "Workflows" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cuffcompare", + "Galaxy tool ids": [ + "cuffcompare" + ], + "Description": "Galaxy wrappers for the Cuffcompare tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cuffcompare", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cuffdiff", + "Galaxy tool ids": [ + "cuffdiff" + ], + "Description": "Galaxy wrappers for the Cuffdiff tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cuffdiff", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cufflinks", + "Galaxy tool ids": [ + "cufflinks" + ], + "Description": "Galaxy wrappers for the Cufflinks tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cufflinks", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cuffmerge", + "Galaxy tool ids": [ + "cuffmerge" + ], + "Description": "Galaxy wrappers for the Cuffmerge tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cuffmerge", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "cuffnorm", + "Galaxy tool ids": [ + "cuffnorm" + ], + "Description": "The Cuffnorm tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cuffnorm", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cuffquant", + "Galaxy tool ids": [ + "cuffquant" + ], + "Description": "The Cuffquant tool", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://cole-trapnell-lab.github.io/cufflinks/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cuffquant", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant", + "Galaxy wrapper version": "2.2.1", + "Conda id": "cufflinks", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasta_clipping_histogram", + "Galaxy tool ids": [ + "cshl_fasta_clipping_histogram" + ], + "Description": "Length Distribution chart", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Graphics", + "Statistics" + ], + "ToolShed id": "fasta_clipping_histogram", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasta_formatter", + "Galaxy tool ids": [ + "cshl_fasta_formatter" + ], + "Description": "FASTA Width formatter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_formatter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fasta_nucleotide_changer", + "Galaxy tool ids": [ + "cshl_fasta_nucleotides_changer" + ], + "Description": "RNA/DNA converter.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_nucleotide_changer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_quality_boxplot", + "Galaxy tool ids": [ + "cshl_fastq_quality_boxplot" + ], + "Description": "Draw quality score boxplot", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation", + "Graphics", + "Statistics" + ], + "ToolShed id": "fastq_quality_boxplot", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_quality_converter", + "Galaxy tool ids": [ + "cshl_fastq_quality_converter" + ], + "Description": "Quality format converter (ASCII-Numeric)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_quality_converter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_quality_filter", + "Galaxy tool ids": [ + "cshl_fastq_quality_filter" + ], + "Description": "Filter by quality", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_quality_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_to_fasta", + "Galaxy tool ids": [ + "cshl_fastq_to_fasta" + ], + "Description": "FASTQ to FASTA converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Convert Formats" + ], + "ToolShed id": "fastq_to_fasta", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_artifacts_filter", + "Galaxy tool ids": [ + "cshl_fastx_artifacts_filter" + ], + "Description": "Remove sequencing artifacts", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "fastx_artifacts_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_barcode_splitter", + "Galaxy tool ids": [ + "cshl_fastx_barcode_splitter" + ], + "Description": "Barcode Splitter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "fastx_barcode_splitter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_clipper", + "Galaxy tool ids": [ + "cshl_fastx_clipper" + ], + "Description": "Clip adapter sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "fastx_clipper", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_collapser", + "Galaxy tool ids": [ + "cshl_fastx_collapser" + ], + "Description": "Collapse sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fastx_collapser", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_nucleotides_distribution", + "Galaxy tool ids": [ + "cshl_fastx_nucleotides_distribution" + ], + "Description": "Draw nucleotides distribution chart", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation", + "Graphics" + ], + "ToolShed id": "fastx_nucleotides_distribution", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_quality_statistics", + "Galaxy tool ids": [ + "cshl_fastx_quality_statistics" + ], + "Description": "Compute quality statistics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation", + "Statistics" + ], + "ToolShed id": "fastx_quality_statistics", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_renamer", + "Galaxy tool ids": [ + "cshl_fastx_renamer" + ], + "Description": "Rename sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "fastx_renamer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_reverse_complement", + "Galaxy tool ids": [ + "cshl_fastx_reverse_complement" + ], + "Description": "Reverse-Complement", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fastq Manipulation", + "Fasta Manipulation" + ], + "ToolShed id": "fastx_reverse_complement", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastx_trimmer", + "Galaxy tool ids": [ + "cshl_fastx_trimmer" + ], + "Description": "Trim sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://hannonlab.cshl.edu/fastx_toolkit/", + "ToolShed categories": [ + "Fasta Manipulation", + "Fastq Manipulation" + ], + "ToolShed id": "fastx_trimmer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer", + "Galaxy wrapper version": "0.0.14", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_combiner", + "Galaxy tool ids": [ + "fastq_combiner" + ], + "Description": "Combine FASTA and QUAL into FASTQ", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation", + "Fasta Manipulation" + ], + "ToolShed id": "fastq_combiner", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_filter", + "Galaxy tool ids": [ + "fastq_filter" + ], + "Description": "Filter FASTQ reads by quality score and length", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_filter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_groomer", + "Galaxy tool ids": [ + "fastq_groomer" + ], + "Description": "Convert between various FASTQ quality formats.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_groomer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_manipulation", + "Galaxy tool ids": [ + "fastq_manipulation" + ], + "Description": "Manipulate FASTQ reads on various attributes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_manipulation", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_masker_by_quality", + "Galaxy tool ids": [ + "fastq_masker_by_quality" + ], + "Description": "FASTQ Masker by quality score", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_masker_by_quality", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_paired_end_deinterlacer", + "Galaxy tool ids": [ + "fastq_paired_end_deinterlacer" + ], + "Description": "FASTQ de-interlacer on paired end reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_paired_end_deinterlacer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_paired_end_interlacer", + "Galaxy tool ids": [ + "fastq_paired_end_interlacer" + ], + "Description": "FASTQ interlacer on paired end reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_paired_end_interlacer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_paired_end_joiner", + "Galaxy tool ids": [ + "fastq_paired_end_joiner" + ], + "Description": "FASTQ joiner on paired end reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_paired_end_joiner", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_paired_end_splitter", + "Galaxy tool ids": [ + "fastq_paired_end_splitter" + ], + "Description": "FASTQ splitter on joined paired end reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_paired_end_splitter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_stats", + "Galaxy tool ids": [ + "fastq_stats" + ], + "Description": "FASTQ Summary Statistics by column", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_stats", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_to_tabular", + "Galaxy tool ids": [ + "fastq_to_tabular" + ], + "Description": "FASTQ to Tabular converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_to_tabular", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastq_trimmer", + "Galaxy tool ids": [ + "fastq_trimmer" + ], + "Description": "FASTQ Trimmer by quality", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_trimmer", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastqtofasta", + "Galaxy tool ids": [ + "fastq_to_fasta_python" + ], + "Description": "FASTQ to FASTA converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastqtofasta", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tabular_to_fastq", + "Galaxy tool ids": [ + "tabular_to_fastq" + ], + "Description": "Tabular to FASTQ converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproject/sequence_utils", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "tabular_to_fastq", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq", + "Galaxy wrapper version": "1.1.5", + "Conda id": "galaxy_sequence_utils", + "Conda version": "1.1.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "kraken", + "Galaxy tool ids": [ + "kraken-filter", + "kraken-mpa-report", + "kraken-report", + "kraken-translate", + "kraken" + ], + "Description": "Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.", + "bio.tool id": "kraken", + "bio.tool ids": [ + "kraken" + ], + "biii": null, + "bio.tool name": "Kraken", + "bio.tool description": "System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.", + "EDAM operation": [ + "Taxonomic classification" + ], + "EDAM topic": [ + "Taxonomy", + "Metagenomics" + ], + "Status": "To update", + "Source": "http://ccb.jhu.edu/software/kraken/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kraken", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken", + "Galaxy wrapper version": null, + "Conda id": "kraken", + "Conda version": "1.1.1", + "EDAM operation (no superclasses)": [ + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy", + "Metagenomics" + ], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "kraken2", + "Galaxy tool ids": [ + "kraken2" + ], + "Description": "Kraken2 for taxonomic designation.", + "bio.tool id": "kraken2", + "bio.tool ids": [ + "kraken2" + ], + "biii": null, + "bio.tool name": "kraken2", + "bio.tool description": "Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.", + "EDAM operation": [ + "Taxonomic classification" + ], + "EDAM topic": [ + "Taxonomy", + "Metagenomics" + ], + "Status": "To update", + "Source": "http://ccb.jhu.edu/software/kraken/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "kraken2", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2", + "Galaxy wrapper version": "2.1.1", + "Conda id": "kraken2", + "Conda version": "2.1.3", + "EDAM operation (no superclasses)": [ + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Taxonomy", + "Metagenomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "samtools", + "Galaxy tool ids": [], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/samtools/samtools", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools", + "Galaxy wrapper version": "1.15.1", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snpeff", + "Galaxy tool ids": [ + "snpEff", + "snpEff_build_gb", + "snpEff_databases", + "snpEff_download", + "snpEff_get_chr_names" + ], + "Description": "SnpEff is a genetic variant annotation and effect prediction toolbox", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/", + "ToolShed categories": [ + "Genome-Wide Association Study", + "Variant Analysis" + ], + "ToolShed id": "snpeff", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff", + "Galaxy wrapper version": null, + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "snpsift", + "Galaxy tool ids": [ + "snpSift_annotate", + "snpSift_caseControl", + "snpSift_extractFields", + "snpSift_filter", + "snpSift_int", + "snpSift_rmInfo", + "snpsift_vartype", + "snpSift_vcfCheck" + ], + "Description": "snpEff SnpSift tools from Pablo Cingolani", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/SnpSift.html", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snpsift", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift", + "Galaxy wrapper version": null, + "Conda id": "snpsift", + "Conda version": "5.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 8, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 8 + }, + { + "Galaxy wrapper id": "snpsift_dbnsfp", + "Galaxy tool ids": [ + "snpSift_dbnsfp" + ], + "Description": "snpEff SnpSift dbnsfp tool from Pablo Cingolani", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/SnpSift.html#dbNSFP", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snpsift_dbnsfp", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp", + "Galaxy wrapper version": null, + "Conda id": "snpsift", + "Conda version": "5.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snpsift_genesets", + "Galaxy tool ids": [ + "snpSift_geneSets" + ], + "Description": "Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://snpeff.sourceforge.net/SnpSift.html#geneSets", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snpsift_genesets", + "Galaxy wrapper owner": "iuc", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets", + "Galaxy wrapper version": null, + "Conda id": "snpsift", + "Conda version": "5.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vcf2tsv", + "Galaxy tool ids": [ + "vcf2tsv" + ], + "Description": "Converts VCF files into tab-delimited format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis", + "Convert Formats" + ], + "ToolShed id": "vcf2tsv", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfaddinfo", + "Galaxy tool ids": [ + "vcfaddinfo" + ], + "Description": "Adds info fields from the second dataset which are not present in the first dataset.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfaddinfo", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfallelicprimitives", + "Galaxy tool ids": [ + "vcfallelicprimitives" + ], + "Description": "Splits alleleic primitives (gaps or mismatches) into multiple VCF lines", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfallelicprimitives", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfannotate", + "Galaxy tool ids": [ + "vcfannotate" + ], + "Description": "Intersect VCF records with BED annotations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfannotate", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfannotategenotypes", + "Galaxy tool ids": [ + "vcfannotategenotypes" + ], + "Description": "Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfannotategenotypes", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfbedintersect", + "Galaxy tool ids": [ + "vcfbedintersect" + ], + "Description": "Intersect VCF and BED datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfbedintersect", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfbreakcreatemulti", + "Galaxy tool ids": [ + "vcfbreakcreatemulti" + ], + "Description": "Break multiple alleles into multiple records, or combine overallpoing alleles into a single record", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfbreakcreatemulti", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfcheck", + "Galaxy tool ids": [ + "vcfcheck" + ], + "Description": "Verify that the reference allele matches the reference genome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfcheck", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfcombine", + "Galaxy tool ids": [ + "vcfcombine" + ], + "Description": "Combine multiple VCF datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfcombine", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfcommonsamples", + "Galaxy tool ids": [ + "vcfcommonsamples" + ], + "Description": "Output records belonging to samples commong between two datasets.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfcommonsamples", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfdistance", + "Galaxy tool ids": [ + "vcfdistance" + ], + "Description": "Calculate distance to the nearest variant.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfdistance", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcffilter", + "Galaxy tool ids": [ + "vcffilter2" + ], + "Description": "Tool for filtering VCF files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcffilter", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcffixup", + "Galaxy tool ids": [ + "vcffixup" + ], + "Description": "Count the allele frequencies across alleles present in each record in the VCF file.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcffixup", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfflatten", + "Galaxy tool ids": [ + "vcfflatten2" + ], + "Description": "Removes multi-allelic sites by picking the most common alternate", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfflatten", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfgeno2haplo", + "Galaxy tool ids": [ + "vcfgeno2haplo" + ], + "Description": "Convert genotype-based phased alleles into haplotype alleles", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfgeno2haplo", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfgenotypes", + "Galaxy tool ids": [ + "vcfgenotypes" + ], + "Description": "Convert numerical representation of genotypes to allelic.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfgenotypes", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfhethom", + "Galaxy tool ids": [ + "vcfhethom" + ], + "Description": "Count the number of heterozygotes and alleles, compute het/hom ratio.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfhethom", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfleftalign", + "Galaxy tool ids": [ + "vcfleftalign" + ], + "Description": "Left-align indels and complex variants in VCF dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfleftalign", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfprimers", + "Galaxy tool ids": [ + "vcfprimers" + ], + "Description": "Extract flanking sequences for each VCF record", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfprimers", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfrandomsample", + "Galaxy tool ids": [ + "vcfrandomsample" + ], + "Description": "Randomly sample sites from VCF dataset", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfrandomsample", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfselectsamples", + "Galaxy tool ids": [ + "vcfselectsamples" + ], + "Description": "Select samples from a VCF file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfselectsamples", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfsort", + "Galaxy tool ids": [ + "vcfsort" + ], + "Description": "Sort VCF dataset by coordinate", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfsort", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "vcfvcfintersect", + "Galaxy tool ids": [ + "vcfvcfintersect" + ], + "Description": "Intersect two VCF datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ekg/vcflib", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "vcfvcfintersect", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect", + "Galaxy wrapper version": null, + "Conda id": "vcflib", + "Conda version": "1.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ThermoRawFileParser", + "Galaxy tool ids": [ + "thermo_raw_file_converter" + ], + "Description": "Thermo RAW file converter", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/compomics/ThermoRawFileParser", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "thermo_raw_file_converter", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser", + "Galaxy wrapper version": "1.3.4", + "Conda id": "thermorawfileparser", + "Conda version": "1.4.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "appendfdr", + "Galaxy tool ids": [ + "append_fdr" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "appendfdr", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr", + "Galaxy wrapper version": "0.2.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bed_to_protein_map", + "Galaxy tool ids": [ + "bed_to_protein_map" + ], + "Description": "Converts a BED file to a tabular list of exon locations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "bed_to_protein_map", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast_plus_remote_blastp", + "Galaxy tool ids": [ + "blast_plus_remote_blastp" + ], + "Description": "NCBI BLAST+ with -remote option", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://blast.ncbi.nlm.nih.gov/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "blast_plus_remote_blastp", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp", + "Galaxy wrapper version": "2.6.0", + "Conda id": "blast", + "Conda version": "2.15.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bumbershoot", + "Galaxy tool ids": [ + "idpqonvertEmbedder", + "idpassemble", + "idpqonvert", + "idpquery", + "myrimatch" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://proteowizard.sourceforge.net/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot", + "Galaxy wrapper version": "3.0.21142", + "Conda id": "bumbershoot", + "Conda version": "3_0_21142_0e4f4a4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "calisp", + "Galaxy tool ids": [ + "calisp" + ], + "Description": "Calgary approach to isotopes in proteomics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/kinestetika/Calisp/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "calisp", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp", + "Galaxy wrapper version": "3.0.13", + "Conda id": "calisp", + "Conda version": "3.0.13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cardinal", + "Galaxy tool ids": [ + "cardinal_classification", + "cardinal_colocalization", + "cardinal_combine", + "cardinal_data_exporter", + "cardinal_filtering", + "cardinal_mz_images", + "cardinal_preprocessing", + "cardinal_quality_report", + "cardinal_segmentations", + "cardinal_single_ion_segmentation", + "cardinal_spectra_plots" + ], + "Description": "Statistical and computational tools for analyzing mass spectrometry imaging datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://cardinalmsi.org", + "ToolShed categories": [ + "Proteomics", + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal", + "Galaxy wrapper version": "2.10.0", + "Conda id": "bioconductor-cardinal", + "Conda version": "3.4.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 9, + "Available on UseGalaxy.eu": 11, + "Available on UseGalaxy.org.fr": 11 + }, + { + "Galaxy wrapper id": "dbbuilder", + "Galaxy tool ids": [ + "dbbuilder" + ], + "Description": "Protein Database Downloader", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "dbbuilder", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder", + "Galaxy wrapper version": "0.3.4", + "Conda id": "wget", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "decoyfasta", + "Galaxy tool ids": [], + "Description": "Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "decoyfasta", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dia_umpire", + "Galaxy tool ids": [ + "dia_umpire_se" + ], + "Description": "DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://diaumpire.sourceforge.net/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "dia_umpire", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire", + "Galaxy wrapper version": "2.1.3", + "Conda id": "dia_umpire", + "Conda version": "2.1.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dialignr", + "Galaxy tool ids": [ + "dialignr" + ], + "Description": "DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/shubham1637/DIAlignR", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "dialignr", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr", + "Galaxy wrapper version": "1.2.0", + "Conda id": "bioconductor-dialignr", + "Conda version": "2.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "diann", + "Galaxy tool ids": [ + "diann" + ], + "Description": "DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/vdemichev/DiaNN", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "diann", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/vdemichev/DiaNN", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann", + "Galaxy wrapper version": "1.8.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "diapysef", + "Galaxy tool ids": [ + "diapysef" + ], + "Description": "diapysef is a convenience package for working with DIA-PASEF data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pypi.org/project/diapysef/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "diapysef", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef", + "Galaxy wrapper version": "0.3.5.0", + "Conda id": "diapysef", + "Conda version": "1.0.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "diffacto", + "Galaxy tool ids": [ + "diffacto" + ], + "Description": "Diffacto comparative protein abundance estimation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/statisticalbiotechnology/diffacto", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "diffacto", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto", + "Galaxy wrapper version": "1.0.6", + "Conda id": "diffacto", + "Conda version": "1.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "digestdb", + "Galaxy tool ids": [ + "digestdb" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "digestdb", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb", + "Galaxy wrapper version": "0.1.0", + "Conda id": "trans_proteomic_pipeline", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "directag_and_tagrecon", + "Galaxy tool ids": [], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "directag_and_tagrecon", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "data_manager_eggnog_mapper", + "Galaxy tool ids": [], + "Description": "downloads eggnog data for eggnog-mapper", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "data_manager_eggnog_mapper", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "data_manager_eggnog_mapper_abspath", + "Galaxy tool ids": [], + "Description": "download eggnog data for eggnog-mapper", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "data_manager_eggnog_mapper_abspath", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "eggnog_mapper", + "Galaxy tool ids": [ + "eggnog_mapper", + "eggnog_mapper_annotate", + "eggnog_mapper_search" + ], + "Description": "eggnog-mapper fast functional annotation of novel sequences", + "bio.tool id": "eggnog-mapper-v2", + "bio.tool ids": [ + "eggnog-mapper-v2" + ], + "biii": null, + "bio.tool name": "eggNOG-mapper v2", + "bio.tool description": "EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.", + "EDAM operation": [ + "Homology-based gene prediction", + "Genome annotation", + "Fold recognition", + "Information extraction", + "Query and retrieval" + ], + "EDAM topic": [ + "Metagenomics", + "Phylogeny", + "Transcriptomics", + "Workflows", + "Sequence analysis" + ], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "eggnog_mapper", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper", + "Galaxy wrapper version": "2.1.8", + "Conda id": "eggnog-mapper", + "Conda version": "2.1.12", + "EDAM operation (no superclasses)": [ + "Homology-based gene prediction", + "Genome annotation", + "Fold recognition", + "Information extraction", + "Query and retrieval" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Phylogeny", + "Transcriptomics", + "Workflows", + "Sequence analysis" + ], + "Available on UseGalaxy.org": 3, + "Available on UseGalaxy.org.au": 3, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "encyclopedia", + "Galaxy tool ids": [ + "encyclopedia_encyclopedia", + "encyclopedia_fasta_to_prosit_csv", + "encyclopedia_library_to_blib", + "encyclopedia_prosit_csv_to_library", + "encyclopedia_quantify", + "encyclopedia_searchtolib", + "encyclopedia_walnut" + ], + "Description": "Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bitbucket.org/searleb/encyclopedia/wiki/Home", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "encyclopedia", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia", + "Galaxy wrapper version": "1.12.34", + "Conda id": "encyclopedia", + "Conda version": "2.12.30", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fasta_merge_files_and_filter_unique_sequences", + "Galaxy tool ids": [ + "fasta_merge_files_and_filter_unique_sequences" + ], + "Description": "Concatenate FASTA database files together", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/tools-galaxyp/", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "fasta_merge_files_and_filter_unique_sequences", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences", + "Galaxy wrapper version": "1.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "fastg2protlib", + "Galaxy tool ids": [ + "fastg2protlib-peptides", + "fastg2protlib-validate" + ], + "Description": "Generate FASTA from FASTG", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/fastg2protlib.git", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "fastg2protlib", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib", + "Galaxy wrapper version": "1.0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "feature_alignment", + "Galaxy tool ids": [ + "feature_alignment" + ], + "Description": "TRIC integrates information from all available runs via a graph-based alignment strategy", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "feature_alignment", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment", + "Galaxy wrapper version": "0.11.0", + "Conda id": "msproteomicstools", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "filter_by_fasta_ids", + "Galaxy tool ids": [ + "filter_by_fasta_ids" + ], + "Description": "Filter FASTA on the headers and/or the sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation", + "Proteomics" + ], + "ToolShed id": "filter_by_fasta_ids", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids", + "Galaxy wrapper version": "2.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "flashlfq", + "Galaxy tool ids": [ + "flashlfq" + ], + "Description": "FlashLFQ mass-spectrometry proteomics label-free quantification", + "bio.tool id": "flashlfq", + "bio.tool ids": [ + "flashlfq" + ], + "biii": null, + "bio.tool name": "FlashLFQ", + "bio.tool description": "FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.", + "EDAM operation": [ + "Label-free quantification" + ], + "EDAM topic": [ + "Proteomics experiment", + "Proteomics" + ], + "Status": "To update", + "Source": "https://github.com/smith-chem-wisc/FlashLFQ", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "flashlfq", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq", + "Galaxy wrapper version": "1.0.3.1", + "Conda id": "flashlfq", + "Conda version": "1.2.6", + "EDAM operation (no superclasses)": [ + "Label-free quantification" + ], + "EDAM topic (no superclasses)": [ + "Proteomics experiment", + "Proteomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gffcompare_to_bed", + "Galaxy tool ids": [ + "gffcompare_to_bed" + ], + "Description": "Filter and convert a gffCompare GTF to BED", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/gpertea/gffcompare/", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "gffcompare_to_bed", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed", + "Galaxy wrapper version": "0.2.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hardklor", + "Galaxy tool ids": [ + "hardklor", + "kronik" + ], + "Description": "Hardklör", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "hardklor", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor", + "Galaxy wrapper version": "2.30.1+galaxy1", + "Conda id": "hardklor", + "Conda version": "2.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "idconvert", + "Galaxy tool ids": [ + "idconvert" + ], + "Description": "Convert mass spectrometry identification files on linux or MacOSX", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "idconvert", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert", + "Galaxy wrapper version": null, + "Conda id": "proteowizard", + "Conda version": "3_0_9992", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "lfq_protein_quant", + "Galaxy tool ids": [ + "lfq_protein_quant" + ], + "Description": "Enable protein summarisation and quantitation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/compomics/LFQ_galaxy_p", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "lfq_protein_quant", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant", + "Galaxy wrapper version": "1.0", + "Conda id": "bioconductor-msnbase", + "Conda version": "2.28.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ltq_iquant_cli", + "Galaxy tool ids": [], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "ltq_iquant_cli", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "maldiquant", + "Galaxy tool ids": [ + "maldi_quant_peak_detection", + "maldi_quant_preprocessing" + ], + "Description": "MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://strimmerlab.org/software/maldiquant/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "MALDIquant", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant", + "Galaxy wrapper version": "1.22.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "map_peptides_to_bed", + "Galaxy tool ids": [ + "map_peptides_to_bed" + ], + "Description": "Map peptides to a reference genome for display by a genome browser", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "map_peptides_to_bed", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed", + "Galaxy wrapper version": "0.2", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "maxquant", + "Galaxy tool ids": [ + "maxquant", + "maxquant_mqpar" + ], + "Description": "wrapper for MaxQuant", + "bio.tool id": "maxquant", + "bio.tool ids": [ + "maxquant" + ], + "biii": null, + "bio.tool name": "MaxQuant", + "bio.tool description": "Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.", + "EDAM operation": [ + "Imputation", + "Visualisation", + "Protein quantification", + "Statistical calculation", + "Standardisation and normalisation", + "Heat map generation", + "Clustering", + "Principal component plotting" + ], + "EDAM topic": [ + "Proteomics experiment", + "Proteomics", + "Statistics and probability" + ], + "Status": "Up-to-date", + "Source": "https://www.maxquant.org/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "maxquant", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant", + "Galaxy wrapper version": "2.0.3.0", + "Conda id": "maxquant", + "Conda version": "2.0.3.0", + "EDAM operation (no superclasses)": [ + "Imputation", + "Visualisation", + "Protein quantification", + "Standardisation and normalisation", + "Heat map generation", + "Clustering" + ], + "EDAM topic (no superclasses)": [ + "Proteomics experiment", + "Proteomics", + "Statistics and probability" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "meta_proteome_analyzer", + "Galaxy tool ids": [ + "meta_proteome_analyzer" + ], + "Description": "MetaProteomeAnalyzer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/compomics/meta-proteome-analyzer/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "meta_proteome_analyzer", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer", + "Galaxy wrapper version": "2.0.0", + "Conda id": "mpa-portable", + "Conda version": "2.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metagene_annotator", + "Galaxy tool ids": [ + "metagene_annotator" + ], + "Description": "MetaGeneAnnotator gene-finding program for prokaryote and phage", + "bio.tool id": "metageneannotator", + "bio.tool ids": [ + "metageneannotator" + ], + "biii": null, + "bio.tool name": "MetaGeneAnnotator", + "bio.tool description": "Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.", + "EDAM operation": [ + "Sequence annotation" + ], + "EDAM topic": [ + "Genomics", + "Model organisms", + "Data submission, annotation and curation" + ], + "Status": "Up-to-date", + "Source": "http://metagene.nig.ac.jp/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "metagene_annotator", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator", + "Galaxy wrapper version": "1.0", + "Conda id": "metagene_annotator", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [ + "Sequence annotation" + ], + "EDAM topic (no superclasses)": [ + "Genomics", + "Model organisms", + "Data submission, annotation and curation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metanovo", + "Galaxy tool ids": [ + "metanovo" + ], + "Description": "Produce targeted databases for mass spectrometry analysis.", + "bio.tool id": "metanovo", + "bio.tool ids": [ + "metanovo" + ], + "biii": null, + "bio.tool name": "MetaNovo", + "bio.tool description": "An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.", + "EDAM operation": [ + "Target-Decoy", + "de Novo sequencing", + "Tag-based peptide identification", + "Protein identification", + "Expression analysis" + ], + "EDAM topic": [ + "Proteomics", + "Microbial ecology", + "Metagenomics", + "Proteomics experiment", + "Small molecules" + ], + "Status": "Up-to-date", + "Source": "https://github.com/uct-cbio/proteomics-pipelines", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "metanovo", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo", + "Galaxy wrapper version": "1.9.4", + "Conda id": "metanovo", + "Conda version": "1.9.4", + "EDAM operation (no superclasses)": [ + "Target-Decoy", + "de Novo sequencing", + "Tag-based peptide identification", + "Protein identification", + "Expression analysis" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Microbial ecology", + "Metagenomics", + "Proteomics experiment", + "Small molecules" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "metaquantome", + "Galaxy tool ids": [ + "metaquantome_db", + "metaquantome_expand", + "metaquantome_filter", + "metaquantome_sample", + "metaquantome_stat", + "metaquantome_viz" + ], + "Description": "quantitative analysis of microbiome taxonomy and function", + "bio.tool id": "metaQuantome", + "bio.tool ids": [ + "metaQuantome" + ], + "biii": null, + "bio.tool name": "metaQuantome", + "bio.tool description": "metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.", + "EDAM operation": [ + "Principal component visualisation", + "Visualisation", + "Functional clustering", + "Query and retrieval", + "Differential protein expression analysis", + "Heat map generation", + "Quantification", + "Indexing", + "Filtering", + "Statistical inference" + ], + "EDAM topic": [ + "Proteomics", + "Metatranscriptomics", + "Microbial ecology", + "Proteomics experiment", + "Metagenomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/galaxyproteomics/metaquantome/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "metaquantome", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome", + "Galaxy wrapper version": "2.0.2", + "Conda id": "metaquantome", + "Conda version": "2.0.2", + "EDAM operation (no superclasses)": [ + "Principal component visualisation", + "Functional clustering", + "Query and retrieval", + "Heat map generation", + "Quantification", + "Indexing", + "Filtering", + "Statistical inference" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Metatranscriptomics", + "Microbial ecology", + "Proteomics experiment", + "Metagenomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 6, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mgf_formatter", + "Galaxy tool ids": [ + "mgf_formatter" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "mgf_formatter", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter", + "Galaxy wrapper version": "1.0.0", + "Conda id": "mgf-formatter", + "Conda version": "1.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "moFF", + "Galaxy tool ids": [ + "proteomics_moff" + ], + "Description": "moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/compomics/moFF", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomics_moff", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF", + "Galaxy wrapper version": "2.0.3", + "Conda id": "moff", + "Conda version": "2.0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "morpheus", + "Galaxy tool ids": [ + "morpheus" + ], + "Description": "Morpheus MS Search Application", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "morpheus", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus", + "Galaxy wrapper version": "2.255.0", + "Conda id": "morpheus", + "Conda version": "288", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mqppep", + "Galaxy tool ids": [ + "mqppep_anova", + "mqppep_preproc" + ], + "Description": "MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/tools-galaxyp/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "mqppep", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep", + "Galaxy wrapper version": "0.1.19", + "Conda id": "bioconductor-preprocesscore", + "Conda version": "1.64.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "msconvert", + "Galaxy tool ids": [ + "msconvert" + ], + "Description": "msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container", + "bio.tool id": "msconvert", + "bio.tool ids": [ + "msconvert" + ], + "biii": null, + "bio.tool name": "msConvert", + "bio.tool description": "msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.", + "EDAM operation": [ + "Filtering", + "Formatting" + ], + "EDAM topic": [ + "Proteomics", + "Proteomics experiment" + ], + "Status": "To update", + "Source": "http://proteowizard.sourceforge.net/tools.shtml", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "msconvert", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert", + "Galaxy wrapper version": "3.0.20287", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Filtering", + "Formatting" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Proteomics experiment" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "msgfplus", + "Galaxy tool ids": [ + "msgfplus" + ], + "Description": "MSGF+", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "msgfplus", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus", + "Galaxy wrapper version": "0.5", + "Conda id": "msgf_plus", + "Conda version": "2024.03.26", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "msms_extractor", + "Galaxy tool ids": [ + "msms_extractor" + ], + "Description": "Extract MS/MS scans from the mzML file(s) based on PSM report.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "msms_extractor", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor", + "Galaxy wrapper version": "1.0.0", + "Conda id": "proteowizard", + "Conda version": "3_0_9992", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "msstats", + "Galaxy tool ids": [ + "msstats" + ], + "Description": "MSstats tool for analyzing mass spectrometry proteomic datasets", + "bio.tool id": "msstatstmt", + "bio.tool ids": [ + "msstatstmt" + ], + "biii": null, + "bio.tool name": "MSstatsTMT", + "bio.tool description": "Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", + "EDAM operation": [ + "Spectrum calculation", + "Tag-based peptide identification", + "Differential protein expression profiling" + ], + "EDAM topic": [ + "Proteomics", + "Proteomics experiment", + "Protein expression" + ], + "Status": "To update", + "Source": "https://github.com/MeenaChoi/MSstats", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats", + "Galaxy wrapper version": "4.0.0", + "Conda id": "bioconductor-msstats", + "Conda version": "4.10.0", + "EDAM operation (no superclasses)": [ + "Spectrum calculation", + "Tag-based peptide identification", + "Differential protein expression profiling" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Proteomics experiment", + "Protein expression" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "msstatstmt", + "Galaxy tool ids": [ + "msstatstmt" + ], + "Description": "MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://msstats.org/msstatstmt/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "msstatstmt", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt", + "Galaxy wrapper version": "2.0.0", + "Conda id": "bioconductor-msstatstmt", + "Conda version": "2.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mt2mq", + "Galaxy tool ids": [ + "mt2mq" + ], + "Description": "Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "mt2mq", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq", + "Galaxy wrapper version": "1.1.0", + "Conda id": "r-tidyverse", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mz_to_sqlite", + "Galaxy tool ids": [ + "mz_to_sqlite" + ], + "Description": "Creates a SQLite database for proteomics data", + "bio.tool id": "mztosqlite", + "bio.tool ids": [ + "mztosqlite" + ], + "biii": null, + "bio.tool name": "mzToSQLite", + "bio.tool description": "Convert proteomics data files into a SQLite database", + "EDAM operation": [ + "Conversion", + "Peptide database search" + ], + "EDAM topic": [ + "Proteomics", + "Biological databases" + ], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/mzToSQLite", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "mz_to_sqlite", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite", + "Galaxy wrapper version": "2.1.1+galaxy0", + "Conda id": "mztosqlite", + "Conda version": "2.1.1", + "EDAM operation (no superclasses)": [ + "Conversion", + "Peptide database search" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Biological databases" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "openms", + "Galaxy tool ids": [ + "AccurateMassSearch", + "AssayGeneratorMetabo", + "BaselineFilter", + "CVInspector", + "ClusterMassTraces", + "ClusterMassTracesByPrecursor", + "CometAdapter", + "CompNovo", + "CompNovoCID", + "ConsensusID", + "ConsensusMapNormalizer", + "CruxAdapter", + "DTAExtractor", + "DatabaseFilter", + "DatabaseSuitability", + "DeMeanderize", + "Decharger", + "DecoyDatabase", + "Digestor", + "DigestorMotif", + "EICExtractor", + "ERPairFinder", + "Epifany", + "ExternalCalibration", + "FFEval", + "FalseDiscoveryRate", + "FeatureFinderCentroided", + "FeatureFinderIdentification", + "FeatureFinderIsotopeWavelet", + "FeatureFinderMRM", + "FeatureFinderMetabo", + "FeatureFinderMetaboIdent", + "FeatureFinderMultiplex", + "FeatureLinkerLabeled", + "FeatureLinkerUnlabeled", + "FeatureLinkerUnlabeledKD", + "FeatureLinkerUnlabeledQT", + "FidoAdapter", + "FileConverter", + "FileFilter", + "FileInfo", + "FileMerger", + "FuzzyDiff", + "GNPSExport", + "HighResPrecursorMassCorrector", + "IDConflictResolver", + "IDExtractor", + "IDFileConverter", + "IDFilter", + "IDMapper", + "IDMassAccuracy", + "IDMerger", + "IDPosteriorErrorProbability", + "IDRTCalibration", + "IDRipper", + "IDScoreSwitcher", + "IDSplitter", + "InternalCalibration", + "IsobaricAnalyzer", + "LabeledEval", + "LuciphorAdapter", + "MRMMapper", + "MRMPairFinder", + "MRMTransitionGroupPicker", + "MSFraggerAdapter", + "MSGFPlusAdapter", + "MSSimulator", + "MSstatsConverter", + "MaRaClusterAdapter", + "MapAlignerIdentification", + "MapAlignerPoseClustering", + "MapAlignerSpectrum", + "MapAlignerTreeGuided", + "MapNormalizer", + "MapRTTransformer", + "MapStatistics", + "MascotAdapter", + "MascotAdapterOnline", + "MassCalculator", + "MassTraceExtractor", + "MetaProSIP", + "MetaboliteAdductDecharger", + "MetaboliteSpectralMatcher", + "MultiplexResolver", + "MyriMatchAdapter", + "MzMLSplitter", + "MzTabExporter", + "NoiseFilterGaussian", + "NoiseFilterSGolay", + "NovorAdapter", + "NucleicAcidSearchEngine", + "OMSSAAdapter", + "OpenMSDatabasesInfo", + "OpenPepXL", + "OpenPepXLLF", + "OpenSwathAnalyzer", + "OpenSwathAssayGenerator", + "OpenSwathChromatogramExtractor", + "OpenSwathConfidenceScoring", + "OpenSwathDIAPreScoring", + "OpenSwathDecoyGenerator", + "OpenSwathFeatureXMLToTSV", + "OpenSwathFileSplitter", + "OpenSwathMzMLFileCacher", + "OpenSwathRTNormalizer", + "OpenSwathRewriteToFeatureXML", + "OpenSwathWorkflow", + "PSMFeatureExtractor", + "PTModel", + "PeakPickerHiRes", + "PeakPickerIterative", + "PeakPickerWavelet", + "PepNovoAdapter", + "PeptideIndexer", + "PercolatorAdapter", + "PhosphoScoring", + "PrecursorIonSelector", + "PrecursorMassCorrector", + "ProteinInference", + "ProteinQuantifier", + "ProteinResolver", + "QCCalculator", + "QCEmbedder", + "QCExporter", + "QCExtractor", + "QCImporter", + "QCMerger", + "QCShrinker", + "QualityControl", + "RNADigestor", + "RNAMassCalculator", + "RNPxlSearch", + "RNPxlXICFilter", + "RTEvaluation", + "RTModel", + "SeedListGenerator", + "SemanticValidator", + "SequenceCoverageCalculator", + "SimpleSearchEngine", + "SiriusAdapter", + "SpecLibCreator", + "SpecLibSearcher", + "SpectraFilterBernNorm", + "SpectraFilterMarkerMower", + "SpectraFilterNLargest", + "SpectraFilterNormalizer", + "SpectraFilterParentPeakMower", + "SpectraFilterScaler", + "SpectraFilterSqrtMower", + "SpectraFilterThresholdMower", + "SpectraFilterWindowMower", + "SpectraMerger", + "SpectraSTSearchAdapter", + "StaticModification", + "SvmTheoreticalSpectrumGeneratorTrainer", + "TICCalculator", + "TOFCalibration", + "TargetedFileConverter", + "TextExporter", + "TransformationEvaluation", + "TriqlerConverter", + "XFDR", + "XMLValidator", + "XTandemAdapter" + ], + "Description": "OpenMS Suite for LC/MS data management and analyses", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.openms.de/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "openms", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms", + "Galaxy wrapper version": "2.8", + "Conda id": "openms", + "Conda version": "3.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 8, + "Available on UseGalaxy.org.au": 35, + "Available on UseGalaxy.eu": 160, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pathwaymatcher", + "Galaxy tool ids": [ + "reactome_pathwaymatcher" + ], + "Description": "Reactome Pathway Matcher", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/LuisFranciscoHS/PathwayMatcher", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "reactome_pathwaymatcher", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher", + "Galaxy wrapper version": null, + "Conda id": "pathwaymatcher", + "Conda version": "1.9.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pep_pointer", + "Galaxy tool ids": [ + "pep_pointer" + ], + "Description": "PepPointer categorizes peptides by their genomic coordinates.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Genomic Interval Operations", + "Proteomics" + ], + "ToolShed id": "pep_pointer", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer", + "Galaxy wrapper version": "0.1.3+galaxy1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pepquery", + "Galaxy tool ids": [ + "pepquery" + ], + "Description": "A peptide-centric MS search engine for novel peptide identification and validation.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pepquery.org", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "pepquery", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery", + "Galaxy wrapper version": "1.6.2", + "Conda id": "pepquery", + "Conda version": "2.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pepquery2", + "Galaxy tool ids": [ + "pepquery2", + "pepquery2_index", + "pepquery2_show_sets" + ], + "Description": "PepQuery2 peptide-centric MS search for peptide identification and validation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://pepquery.org", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "pepquery2", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2", + "Galaxy wrapper version": "2.0.2", + "Conda id": "pepquery", + "Conda version": "2.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "peptide_genomic_coordinate", + "Galaxy tool ids": [ + "peptide_genomic_coordinate" + ], + "Description": "Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "peptide_genomic_coordinate", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate", + "Galaxy wrapper version": "1.0.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "peptideshaker", + "Galaxy tool ids": [ + "fasta_cli", + "ident_params", + "peptide_shaker", + "search_gui" + ], + "Description": "PeptideShaker and SearchGUI", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://compomics.github.io", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "peptideshaker", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker", + "Galaxy wrapper version": null, + "Conda id": "searchgui", + "Conda version": "4.3.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "pepxml_to_xls", + "Galaxy tool ids": [], + "Description": "Convert PepXML to Tabular", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "pepxml_to_xls", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "percolator", + "Galaxy tool ids": [ + "batched_set_list_creator", + "percolator", + "percolator_input_converters", + "pout2mzid" + ], + "Description": "Percolator", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "percolator", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator", + "Galaxy wrapper version": "3.5", + "Conda id": "percolator", + "Conda version": "3.6.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pi_db_tools", + "Galaxy tool ids": [ + "calc_delta_pi", + "pi_db_split", + "pi_dbspec_align" + ], + "Description": "HiRIEF tools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "hirieftools", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools", + "Galaxy wrapper version": "1.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pmd_fdr", + "Galaxy tool ids": [ + "pmd_fdr" + ], + "Description": "Calculate Precursor Mass Discrepancy (PMD) for MS/MS", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/slhubler/PMD-FDR-for-Galaxy-P", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "pmd_fdr", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr", + "Galaxy wrapper version": "1.4.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "custom_pro_db", + "Galaxy tool ids": [ + "custom_pro_db" + ], + "Description": "CustomProDB", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/customProDB.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "custom_pro_db", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db", + "Galaxy wrapper version": "1.22.0", + "Conda id": "bioconductor-rgalaxy", + "Conda version": "1.37.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "custom_pro_db_annotation_data_manager", + "Galaxy tool ids": [], + "Description": "CustomProDB Annotation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/customProDB.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "custom_pro_db_annotation_data_manager", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "psm2sam", + "Galaxy tool ids": [ + "PSMtoSAM" + ], + "Description": "PSM to SAM", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://bioconductor.org/packages/release/bioc/html/proBAMr.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "psm_to_sam", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam", + "Galaxy wrapper version": "1.3.2.1", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "proteinpilot", + "Galaxy tool ids": [ + "convert_windows_newlines", + "proteinpilot", + "proteinpilot_group_extractor", + "proteinpilot_tabular", + "proteinpilot_xml" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "proteinpilot", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot", + "Galaxy wrapper version": "0.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "retrieve_ensembl_bed", + "Galaxy tool ids": [ + "retrieve_ensembl_bed" + ], + "Description": "Retrieve cDNA features from Ensembl REST API in BED format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rest.ensembl.org/", + "ToolShed categories": [ + "Data Source" + ], + "ToolShed id": "retrieve_ensembl_bed", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed", + "Galaxy wrapper version": "0.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "translate_bed", + "Galaxy tool ids": [ + "translate_bed" + ], + "Description": "Translate BED transcript CDS or cDNA in 3 frames", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://rest.ensembl.org/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "translate_bed", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed", + "Galaxy wrapper version": "0.1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_joinquantpepionswithproteins", + "Galaxy tool ids": [ + "proteomiqon_joinquantpepionswithproteins" + ], + "Description": "The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_joinquantpepionswithproteins", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins", + "Galaxy wrapper version": "0.0.1", + "Conda id": "proteomiqon-joinquantpepionswithproteins", + "Conda version": "0.0.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_labeledproteinquantification", + "Galaxy tool ids": [ + "proteomiqon_labeledproteinquantification" + ], + "Description": "The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_labeledproteinquantification", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification", + "Galaxy wrapper version": "0.0.1", + "Conda id": "proteomiqon-labeledproteinquantification", + "Conda version": "0.0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_labelfreeproteinquantification", + "Galaxy tool ids": [ + "proteomiqon_labelfreeproteinquantification" + ], + "Description": "The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_labelfreeproteinquantification", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification", + "Galaxy wrapper version": "0.0.1", + "Conda id": "proteomiqon-labelfreeproteinquantification", + "Conda version": "0.0.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_mzmltomzlite", + "Galaxy tool ids": [ + "proteomiqon_mzmltomzlite" + ], + "Description": "The tool MzMLToMzLite allows to convert mzML files to mzLite files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_mzmltomzlite", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite", + "Galaxy wrapper version": "0.0.8", + "Conda id": "proteomiqon-mzmltomzlite", + "Conda version": "0.0.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_peptidedb", + "Galaxy tool ids": [ + "proteomiqon_peptidedb" + ], + "Description": "The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_peptidedb", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb", + "Galaxy wrapper version": "0.0.7", + "Conda id": "proteomiqon-peptidedb", + "Conda version": "0.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_peptidespectrummatching", + "Galaxy tool ids": [ + "proteomiqon_peptidespectrummatching" + ], + "Description": "Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_peptidespectrummatching", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching", + "Galaxy wrapper version": "0.0.7", + "Conda id": "proteomiqon-peptidespectrummatching", + "Conda version": "0.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_proteininference", + "Galaxy tool ids": [ + "proteomiqon_proteininference" + ], + "Description": "MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_proteininference", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference", + "Galaxy wrapper version": "0.0.7", + "Conda id": "proteomiqon-proteininference", + "Conda version": "0.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_psmbasedquantification", + "Galaxy tool ids": [ + "proteomiqon_psmbasedquantification" + ], + "Description": "The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_psmbasedquantification", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification", + "Galaxy wrapper version": "0.0.8", + "Conda id": "proteomiqon-psmbasedquantification", + "Conda version": "0.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteomiqon_psmstatistics", + "Galaxy tool ids": [ + "proteomiqon_psmstatistics" + ], + "Description": "The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteomiqon_psmstatistics", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics", + "Galaxy wrapper version": "0.0.8", + "Conda id": "proteomiqon-psmstatistics", + "Conda version": "0.0.8", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "proteore_venn_diagram", + "Galaxy tool ids": [ + "proteore_venn_diagram" + ], + "Description": "ProteoRE JVenn Diagram", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "proteore_venn_diagram", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram", + "Galaxy wrapper version": "2021.06.08", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "protxml_to_xls", + "Galaxy tool ids": [ + "protxml_to_xls" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "protxml_to_xls", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls", + "Galaxy wrapper version": "0.1.0", + "Conda id": "trans_proteomic_pipeline", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "psm_eval", + "Galaxy tool ids": [ + "psm_eval" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "psm_eval", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval", + "Galaxy wrapper version": "0.1.0", + "Conda id": "binaries_for_psm_eval", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "psm_validation", + "Galaxy tool ids": [ + "psmvalidator" + ], + "Description": "Validate PSM from Ion Fragmentation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/psm_fragments.git", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "psm_validation", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation", + "Galaxy wrapper version": "1.0.3", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pyprophet", + "Galaxy tool ids": [ + "pyprophet_export", + "pyprophet_merge", + "pyprophet_peptide", + "pyprophet_protein", + "pyprophet_score", + "pyprophet_subsample" + ], + "Description": "Semi-supervised learning and scoring of OpenSWATH results.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/PyProphet/pyprophet", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet", + "Galaxy wrapper version": "2.1.4", + "Conda id": "pyprophet", + "Conda version": "2.2.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pyteomics", + "Galaxy tool ids": [ + "mztab2tsv" + ], + "Description": "Tools using the pyteomics library", + "bio.tool id": "pyteomics", + "bio.tool ids": [ + "pyteomics" + ], + "biii": null, + "bio.tool name": "Pyteomics", + "bio.tool description": "Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.", + "EDAM operation": [ + "Protein identification" + ], + "EDAM topic": [ + "Proteomics", + "Proteomics experiment" + ], + "Status": "To update", + "Source": "https://pyteomics.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Proteomics", + "Metabolomics" + ], + "ToolShed id": "pyteomics", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics", + "Galaxy wrapper version": "4.4.1", + "Conda id": "pyteomics", + "Conda version": "4.7.2", + "EDAM operation (no superclasses)": [ + "Protein identification" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Proteomics experiment" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "quantp", + "Galaxy tool ids": [ + "quantp" + ], + "Description": "Correlation between protein and transcript abundance", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "quantp", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp", + "Galaxy wrapper version": "1.1.2", + "Conda id": "r-data.table", + "Conda version": "1.11.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "quantwiz_iq", + "Galaxy tool ids": [ + "quantwiz_iq" + ], + "Description": "Isobaric Quantitation using QuantWiz-IQ", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://sourceforge.net/projects/quantwiz/", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "quantwiz_iq", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq", + "Galaxy wrapper version": "2.0", + "Conda id": "quantwiz-iq", + "Conda version": "2.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qupath_roi_splitter", + "Galaxy tool ids": [ + "qupath_roi_splitter" + ], + "Description": "Split ROI coordinates of QuPath TMA annotation by cell type", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/npinter/ROIsplitter", + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "qupath_roi_splitter", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "hhttps://github.com/npinter/ROIsplitter", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter", + "Galaxy wrapper version": "0.2.1", + "Conda id": "geojson", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rawtools", + "Galaxy tool ids": [ + "rawtools" + ], + "Description": "Raw Tools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/kevinkovalchik/RawTools", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "rawtools", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools", + "Galaxy wrapper version": null, + "Conda id": "rawtools", + "Conda version": "2.0.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "regex_find_replace", + "Galaxy tool ids": [ + "regex1", + "regexColumn1" + ], + "Description": "Use python regular expressions to find and replace text", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "regex_find_replace", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace", + "Galaxy wrapper version": "1.0.3", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "scaffold", + "Galaxy tool ids": [ + "scaffold", + "scaffold_export" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [], + "ToolShed id": "scaffold", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold", + "Galaxy wrapper version": "0.1.0", + "Conda id": "scaffold", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sixgill", + "Galaxy tool ids": [ + "sixgill_build", + "sixgill_filter", + "sixgill_makefasta", + "sixgill_merge" + ], + "Description": "Six-frame Genome-Inferred Libraries for LC-MS/MS", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": null, + "ToolShed categories": [ + "Proteomics", + "MetaProteomics" + ], + "ToolShed id": "sixgill", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill", + "Galaxy wrapper version": "0.2.4", + "Conda id": "sixgill", + "Conda version": "0.2.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spectrast2spectrast_irt", + "Galaxy tool ids": [ + "gp_spectrast2spectrast_irt" + ], + "Description": "Filter from spectraST files to swath input files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "spectrast2spectrast_irt", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt", + "Galaxy wrapper version": "0.1.0", + "Conda id": "msproteomicstools", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spectrast2tsv", + "Galaxy tool ids": [ + "gp_spectrast2tsv" + ], + "Description": "Filter from spectraST files to swath input files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "spectrast2tsv", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv", + "Galaxy wrapper version": "0.1.0", + "Conda id": "msproteomicstools", + "Conda version": "0.11.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "translate_bed_sequences", + "Galaxy tool ids": [ + "translate_bed_sequences" + ], + "Description": "Perform 3 frame translation of BED file augmented with a sequence column", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "translate_bed_sequences", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences", + "Galaxy wrapper version": "0.2.0", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "unipept", + "Galaxy tool ids": [ + "unipept" + ], + "Description": "Unipept retrieves metaproteomics information", + "bio.tool id": "unipept", + "bio.tool ids": [ + "unipept" + ], + "biii": null, + "bio.tool name": "Unipept", + "bio.tool description": "Metaproteomics data analysis with a focus on interactive data visualizations.", + "EDAM operation": [ + "Prediction and recognition", + "Visualisation" + ], + "EDAM topic": [ + "Proteomics", + "Proteogenomics", + "Biodiversity", + "Workflows" + ], + "Status": "To update", + "Source": "https://github.com/galaxyproteomics/tools-galaxyp", + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "unipept", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://unipept.ugent.be/apidocs", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept", + "Galaxy wrapper version": "4.5.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Prediction and recognition", + "Visualisation" + ], + "EDAM topic (no superclasses)": [ + "Proteomics", + "Proteogenomics", + "Biodiversity", + "Workflows" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "uniprotxml_downloader", + "Galaxy tool ids": [ + "uniprotxml_downloader" + ], + "Description": "Download UniProt proteome in XML or fasta format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Proteomics" + ], + "ToolShed id": "uniprotxml_downloader", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader", + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader", + "Galaxy wrapper version": "2.4.0", + "Conda id": "requests", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "validate_fasta_database", + "Galaxy tool ids": [ + "validate_fasta_database" + ], + "Description": "runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Fasta Manipulation", + "Proteomics" + ], + "ToolShed id": "validate_fasta_database", + "Galaxy wrapper owner": "galaxyp", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database", + "Galaxy wrapper version": "0.1.5", + "Conda id": "validate-fasta-database", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bio3d", + "Galaxy tool ids": [ + "bio3d_dccm", + "bio3d_pca", + "bio3d_rmsd", + "bio3d_rmsf", + "bio3d_pca_visualize" + ], + "Description": "Bio3d is a program that can be used to analyse molecular dynamics trajectories.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://thegrantlab.org/bio3d/index.php", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "bio3d", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d", + "Galaxy wrapper version": "2.4_1", + "Conda id": "r-bio3d", + "Conda version": "2.3_3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 4, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "biomoldyn", + "Galaxy tool ids": [ + "biomd_neqgamma", + "fastpca", + "biomd_extract_clusters", + "biomd_rmsd_clustering" + ], + "Description": "Tools for MD analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/moldyn/", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "biomoldyn", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn", + "Galaxy wrapper version": "1.5.2", + "Conda id": "scipy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ambertools", + "Galaxy tool ids": [ + "ambertools_acpype", + "acpype_Amber2Gromacs", + "ambertools_antechamber", + "mmpbsa_mmgbsa", + "ambertools_parmchk2", + "parmconv", + "tleap" + ], + "Description": "Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://ambermd.org/AmberTools.php", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "ambertools", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools", + "Galaxy wrapper version": "21.10", + "Conda id": "ambertools", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 7, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "packmol", + "Galaxy tool ids": [ + "packmol" + ], + "Description": "PACKMOL is a package for creating starting structures for Molecular Dynamics simulations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://m3g.iqm.unicamp.br/packmol/home.shtml", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "packmol", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol", + "Galaxy wrapper version": "18.169.1", + "Conda id": "packmol", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "topologyeditors", + "Galaxy tool ids": [ + "gromacs_modify_topology", + "gromacs_extract_topology" + ], + "Description": "Set of python scripts and associated tool files that can be used to modify topology files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "topologyeditors", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors", + "Galaxy wrapper version": "0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "free_energy", + "Galaxy tool ids": [], + "Description": "Free energy tools of BRIDGE.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "freeenergy", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gromacs", + "Galaxy tool ids": [ + "gmx_check", + "gmx_editconf", + "gmx_energy", + "gmx_get_builtin_file", + "gmx_rg", + "gmx_makendx", + "gmx_merge_topology_files", + "gmx_em", + "gmx_restraints", + "gmx_rmsd", + "gmx_rmsf", + "gmx_setup", + "gmx_sim", + "gmx_solvate", + "gmx_trj" + ], + "Description": "GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/gromacs", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "gromacs", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs", + "Galaxy wrapper version": "2022", + "Conda id": "gromacs", + "Conda version": "2021.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 14, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 15, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mdanalysis", + "Galaxy tool ids": [ + "mdanalysis_angle", + "mdanalysis_dihedral", + "mdanalysis_distance", + "mdanalysis_endtoend", + "mdanalysis_extract_rmsd", + "mdanalysis_hbonds", + "mdanalysis_cosine_analysis", + "mdanalysis_ramachandran_protein", + "mdanalysis_ramachandran_plot", + "mdanalysis_rdf" + ], + "Description": "MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/MDAnalysis/mdanalysis", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "mdanalysis", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis", + "Galaxy wrapper version": "1.0.0", + "Conda id": "mdanalysis", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 10, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 10, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mdfileconverter", + "Galaxy tool ids": [ + "md_converter" + ], + "Description": "A tool for interconverting between different MD structure and trajectory file formats.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "md_converter", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter", + "Galaxy wrapper version": "1.9.7", + "Conda id": "mdtraj", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mdslicer", + "Galaxy tool ids": [ + "md_slicer" + ], + "Description": "A tool for slicing trajectory files using MDTraj.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "md_converter", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer", + "Galaxy wrapper version": "1.9.9", + "Conda id": "mdtraj", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mdtraj", + "Galaxy tool ids": [ + "traj_selections_and_merge" + ], + "Description": "MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/mdtraj/mdtraj", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "mdtraj", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj", + "Galaxy wrapper version": "1.9.7", + "Conda id": "mdtraj", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "openmm", + "Galaxy tool ids": [ + "pdbfixer" + ], + "Description": "OpenMM is a toolkit for molecular simulation using high performance GPU code.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/openmm", + "ToolShed categories": [ + "Molecular Dynamics", + "Computational chemistry" + ], + "ToolShed id": "openmm", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm", + "Galaxy wrapper version": "1.8.1", + "Conda id": "pdbfixer", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vmd", + "Galaxy tool ids": [], + "Description": "vmd is a package for visualizing and analyzing trajectories from molecular dynamics (MD) simulations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.ks.uiuc.edu/Research/vmd/", + "ToolShed categories": [ + "Computational chemistry" + ], + "ToolShed id": "vmd", + "Galaxy wrapper owner": "chemteam", + "Galaxy wrapper source": "https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd", + "Galaxy wrapper parsed folder": "https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "artbio_bam_cleaning", + "Galaxy tool ids": [ + "artbio_bam_cleaning" + ], + "Description": "filter bam files before somatic-varscan or lumpy-smoove analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "SAM", + "Variant Analysis" + ], + "ToolShed id": "artbio_bam_cleaning", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning", + "Galaxy wrapper version": "1.10+galaxy0", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bamparse", + "Galaxy tool ids": [ + "bamparse" + ], + "Description": "Generates hit count lists from bam alignments.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Transcriptomics" + ], + "ToolShed id": "bamparse", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse", + "Galaxy wrapper version": "4.1.1", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bigwig_to_bedgraph", + "Galaxy tool ids": [ + "bigwig_to_bedgraph" + ], + "Description": "Converts a bigWig file to bedGraph format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "bigwig_to_bedgraph", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph", + "Galaxy wrapper version": "377+galaxy1", + "Conda id": "ucsc-bigwigtobedgraph", + "Conda version": "448", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "bigwig_to_wig", + "Galaxy tool ids": [ + "bigwig_to_wig" + ], + "Description": "Converts a bigWig file to Wiggle (WIG) format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://artbio.fr", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "bigwig_to_wig", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig", + "Galaxy wrapper version": "3+galaxy0", + "Conda id": "ucsc-bigwiginfo", + "Conda version": "377", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast_to_scaffold", + "Galaxy tool ids": [ + "blast2scaffold" + ], + "Description": "Generate DNA scaffold from blastn or tblastx alignments of Contigs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Sequence Analysis", + "Assembly" + ], + "ToolShed id": "blast_to_scaffold", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold", + "Galaxy wrapper version": "1.1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast_unmatched", + "Galaxy tool ids": [ + "blast_unmatched" + ], + "Description": "Extract unmatched query sequences from blast", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "blast_unmatched", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched", + "Galaxy wrapper version": "1.0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blastparser_and_hits", + "Galaxy tool ids": [ + "BlastParser_and_hits" + ], + "Description": "Parse blast outputs and compile hits", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Assembly", + "RNA" + ], + "ToolShed id": "blastparser_and_hits", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits", + "Galaxy wrapper version": "2.7.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blastx_to_scaffold", + "Galaxy tool ids": [ + "blastx2scaffold" + ], + "Description": "Generate DNA scaffold from blastx alignment of Contigs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Sequence Analysis", + "Assembly" + ], + "ToolShed id": "blastx_to_scaffold", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold", + "Galaxy wrapper version": "1.1.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cap3", + "Galaxy tool ids": [ + "cap3" + ], + "Description": "cap3 wrapper", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Assembly" + ], + "ToolShed id": "cap3", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3", + "Galaxy wrapper version": "2.0.1", + "Conda id": "cap3", + "Conda version": "10.2011", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cherry_pick_fasta", + "Galaxy tool ids": [ + "cherry_pick_fasta" + ], + "Description": "Pick fasta sequence with specific header content", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Fasta Manipulation" + ], + "ToolShed id": "cherry_pick_fasta", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta", + "Galaxy wrapper version": "4.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "concat_multi_datasets", + "Galaxy tool ids": [ + "cat_multi_datasets" + ], + "Description": "Concatenate multiple datasets tail-to-head, including collection datasets.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "concatenate_multiple_datasets", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets", + "Galaxy wrapper version": "1.4.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cpm_tpm_rpk", + "Galaxy tool ids": [ + "cpm_tpm_rpk" + ], + "Description": "Generate CPM,TPM or RPK from raw counts", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "cpm_tpm_rpk", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk", + "Galaxy wrapper version": "0.5.2", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "deseq2_normalization", + "Galaxy tool ids": [ + "deseq2_normalization" + ], + "Description": "Normalizes gene hitlists", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Transcriptomics", + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": "deseq2_normalization", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization", + "Galaxy wrapper version": "1.40.2+galaxy0", + "Conda id": "bioconductor-deseq2", + "Conda version": "1.42.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "embl2fa", + "Galaxy tool ids": [ + "embl2fa" + ], + "Description": "Converts EMBL flat format to fasta format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "embl2fa", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa", + "Galaxy wrapper version": "0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ez_histograms", + "Galaxy tool ids": [ + "ez_histograms" + ], + "Description": "ggplot2 histograms and density plots", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/tidyverse/ggplot2", + "ToolShed categories": [ + "Visualization", + "Statistics" + ], + "ToolShed id": "ez_histograms", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms", + "Galaxy wrapper version": "3.4.4", + "Conda id": "r-ggplot2", + "Conda version": "2.2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fetch_fasta_from_ncbi", + "Galaxy tool ids": [ + "retrieve_fasta_from_NCBI" + ], + "Description": "Fetch fasta sequences from NCBI using eutils wrappers", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Fasta Manipulation", + "Data Source" + ], + "ToolShed id": "fetch_fasta_from_ncbi", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi", + "Galaxy wrapper version": "3.1.0", + "Conda id": "urllib3", + "Conda version": "1.12", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fisher_test", + "Galaxy tool ids": [ + "fishertest" + ], + "Description": "Fisher's exact test on two-column hit lists.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Statistics" + ], + "ToolShed id": "fishertest", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test", + "Galaxy wrapper version": "2.32.0+galaxy0", + "Conda id": "bioconductor-qvalue", + "Conda version": "2.34.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gatk4", + "Galaxy tool ids": [ + "filtermutectcalls", + "mergemutectstats", + "mutect2" + ], + "Description": "Find somatic variations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "gatk4", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4", + "Galaxy wrapper version": "4.1.7.0", + "Conda id": "gatk4", + "Conda version": "4.5.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "get_reference_fasta", + "Galaxy tool ids": [ + "get_fasta_reference" + ], + "Description": "Obtain reference genome sequence.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Data Source", + "Fasta Manipulation" + ], + "ToolShed id": "get_reference_fasta", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta", + "Galaxy wrapper version": "0.3.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_center_scale", + "Galaxy tool ids": [ + "center_scale" + ], + "Description": "Center or scale (standardize) data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Statistics" + ], + "ToolShed id": "gsc_center_scale", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale", + "Galaxy wrapper version": "4.3.1+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_filter_cells", + "Galaxy tool ids": [ + "filter_cells" + ], + "Description": "Filter single cell RNAseq data on libray depth and number of detected genes", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_filter_cells", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells", + "Galaxy wrapper version": "4.3.1+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_filter_genes", + "Galaxy tool ids": [ + "filter_genes" + ], + "Description": "Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_filter_genes", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes", + "Galaxy wrapper version": "4.3.1+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_gene_expression_correlations", + "Galaxy tool ids": [ + "single_cell_gene_expression_correlations" + ], + "Description": "Compute single-cell paire-wise gene expressions correlations", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_gene_expression_correlations", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations", + "Galaxy wrapper version": "4.3.1+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_high_dimensions_visualisation", + "Galaxy tool ids": [ + "high_dimensions_visualisation" + ], + "Description": "Generates PCA, t-SNE and HCPC visualisation", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics", + "Visualization" + ], + "ToolShed id": "gsc_high_dimensions_visualisation", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation", + "Galaxy wrapper version": "4.3+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_mannwhitney_de", + "Galaxy tool ids": [ + "mannwhitney_de" + ], + "Description": "Perform a mann-whitney differential testing between two sets of gene expression data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_mannwhitney_de", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de", + "Galaxy wrapper version": "4.1.3+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_scran_normalize", + "Galaxy tool ids": [ + "scran_normalize" + ], + "Description": "Normalize raw counts using scran", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_scran_normalize", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize", + "Galaxy wrapper version": "1.28.1+galaxy0", + "Conda id": "bioconductor-scran", + "Conda version": "1.30.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gsc_signature_score", + "Galaxy tool ids": [ + "signature_score" + ], + "Description": "Compute signature scores from single cell RNAseq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "gsc_signature_score", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score", + "Galaxy wrapper version": "2.3.9+galaxy0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "guppy", + "Galaxy tool ids": [ + "guppy-basecaller" + ], + "Description": "A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "guppy_basecaller", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy", + "Galaxy wrapper version": "0.2.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "high_dim_heatmap", + "Galaxy tool ids": [ + "high_dim_heatmap" + ], + "Description": "gplot heatmap.2 function adapted for plotting large heatmaps", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/cran/gplots", + "ToolShed categories": [ + "Visualization" + ], + "ToolShed id": "high_dim_heatmap", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap", + "Galaxy wrapper version": "3.1.3+galaxy0", + "Conda id": "r-gplots", + "Conda version": "2.17.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "justdiff", + "Galaxy tool ids": [ + "justdiff" + ], + "Description": "Unix diff", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "justdiff", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff", + "Galaxy wrapper version": "3.10+galaxy0", + "Conda id": "diffutils", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "justgzip", + "Galaxy tool ids": [ + "justgzip" + ], + "Description": "Compress fastq sequence files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "justgzip", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip", + "Galaxy wrapper version": "2.8+galaxy0", + "Conda id": "pigz", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "lumpy_smoove", + "Galaxy tool ids": [ + "lumpy_smoove", + "vcf2hrdetect" + ], + "Description": "Galaxy wrapper of the lumpy-using smoove workflow", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "lumpy_smoove", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove", + "Galaxy wrapper version": "0.2.8+galaxy1", + "Conda id": "svtyper", + "Conda version": "0.7.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "manta", + "Galaxy tool ids": [ + "manta" + ], + "Description": "Structural variant and indel caller for mapped sequencing data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "manta", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/manta", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/manta", + "Galaxy wrapper version": "1.6", + "Conda id": "manta", + "Conda version": "1.6.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mapping_quality_stats", + "Galaxy tool ids": [ + "mapqstatistics" + ], + "Description": "Collects and shows the distribution of MAPQ values in a BAM alignment file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Sequence Analysis", + "Statistics" + ], + "ToolShed id": "mapping_quality_stats", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats", + "Galaxy wrapper version": "0.22.0", + "Conda id": "r-optparse", + "Conda version": "1.3.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mircounts", + "Galaxy tool ids": [ + "mircounts" + ], + "Description": "Generates miRNA count lists from read alignments to mirBase.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Transcriptomics" + ], + "ToolShed id": "mircounts", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts", + "Galaxy wrapper version": "1.6", + "Conda id": "tar", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mutational_patterns", + "Galaxy tool ids": [ + "mutational_patterns" + ], + "Description": "Mutational patterns and signatures in base substitution catalogs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "mutational_patterns", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns", + "Galaxy wrapper version": "3.12.0", + "Conda id": "bioconductor-mutationalpatterns", + "Conda version": "3.12.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "oases", + "Galaxy tool ids": [ + "oasesoptimiserv" + ], + "Description": "Short read assembler", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Assembly", + "RNA" + ], + "ToolShed id": "oases", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/oases", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/oases", + "Galaxy wrapper version": "1.4.0", + "Conda id": "oases", + "Conda version": "0.2.09", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pathifier", + "Galaxy tool ids": [ + "pathifier" + ], + "Description": "pathifier", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://", + "ToolShed categories": [ + "Transcriptomics", + "Statistics" + ], + "ToolShed id": "pathifier", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier", + "Galaxy wrapper version": "1.40.0", + "Conda id": "bioconductor-pathifier", + "Conda version": "1.40.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "pindel", + "Galaxy tool ids": [ + "pindel" + ], + "Description": "Pindel detects genome-wide structural variation.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "pindel", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel", + "Galaxy wrapper version": "0.2.5b9", + "Conda id": "pindel", + "Conda version": "0.2.5b9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "probecoverage", + "Galaxy tool ids": [ + "probecoverage" + ], + "Description": "computes and plots read coverage of genomic regions by sequencing datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Sequence Analysis", + "Genomic Interval Operations", + "Graphics", + "Statistics" + ], + "ToolShed id": "probecoverage", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage", + "Galaxy wrapper version": "0.22.0", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "repenrich", + "Galaxy tool ids": [ + "edger-repenrich", + "repenrich" + ], + "Description": "Repeat element profiling", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "repenrich", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich", + "Galaxy wrapper version": "2.31.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "repenrich2", + "Galaxy tool ids": [ + "edger-repenrich2", + "repenrich2" + ], + "Description": "Repeat element profiling using bowtie2 aligner", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "repenrich2", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2", + "Galaxy wrapper version": "2.31.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rsem", + "Galaxy tool ids": [ + "extract_transcript_to_gene_map_from_trinity", + "purgegtffrommultichromgenes", + "rsembowtie2", + "rsembowtie" + ], + "Description": "transcript quantification from RNA-Seq data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/deweylab/RSEM", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": "rsem", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/artbio/tools-artbio/tree/master/tools/rsem", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem", + "Galaxy wrapper version": null, + "Conda id": "rsem", + "Conda version": "1.3.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sambamba", + "Galaxy tool ids": [ + "sambamba_sample_or_filter" + ], + "Description": "filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "sambamba", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba", + "Galaxy wrapper version": "0.7.1+galaxy1", + "Conda id": "sambamba", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sashimi_plot", + "Galaxy tool ids": [ + "sashimi_plot" + ], + "Description": "Generates a sashimi plot from bam files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Transcriptomics", + "Graphics", + "Visualization" + ], + "ToolShed id": "sashimi_plot", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot", + "Galaxy wrapper version": "0.1.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sequence_format_converter", + "Galaxy tool ids": [ + "sequence_format_converter" + ], + "Description": "various fasta to tabular conversions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Convert Formats", + "Fasta Manipulation" + ], + "ToolShed id": "sequence_format_converter", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter", + "Galaxy wrapper version": "2.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "small_rna_clusters", + "Galaxy tool ids": [ + "small_rna_clusters" + ], + "Description": "clusters small rna reads in alignment BAM files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "SAM", + "Graphics", + "Next Gen Mappers" + ], + "ToolShed id": "small_rna_clusters", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters", + "Galaxy wrapper version": "1.3.0", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "small_rna_maps", + "Galaxy tool ids": [ + "small_rna_maps" + ], + "Description": "Generates small read maps from alignment BAM files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "SAM", + "Graphics", + "Next Gen Mappers" + ], + "ToolShed id": "small_rna_maps", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps", + "Galaxy wrapper version": "3.1.1", + "Conda id": "numpy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "small_rna_signatures", + "Galaxy tool ids": [ + "overlapping_reads", + "signature" + ], + "Description": "Computes the tendency of small RNAs to overlap with each other.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "small_rna_signatures", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures", + "Galaxy wrapper version": "3.4.2", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snvtocnv", + "Galaxy tool ids": [ + "sequenzaindex", + "snvtocnv" + ], + "Description": "infer copy number variations from a vcf file with SNVs using R sequenza", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "snvtocnv", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv", + "Galaxy wrapper version": "3.0.0+galaxy1", + "Conda id": "sequenza-utils", + "Conda version": "3.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sr_bowtie", + "Galaxy tool ids": [ + "bowtieForSmallRNA" + ], + "Description": "bowtie wrapper tool to align small RNA sequencing reads", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Next Gen Mappers" + ], + "ToolShed id": "sr_bowtie", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie", + "Galaxy wrapper version": "2.3.0", + "Conda id": "bowtie", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sr_bowtie_dataset_annotation", + "Galaxy tool ids": [ + "sr_bowtie_dataset_annotation" + ], + "Description": "Maps iteratively small RNA sequencing datasets to reference sequences.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA" + ], + "ToolShed id": "sr_bowtie_dataset_annotation", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation", + "Galaxy wrapper version": "2.8", + "Conda id": "bowtie", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "tarfast5", + "Galaxy tool ids": [ + "tarfast5" + ], + "Description": "produces a tar.gz archive of fast5 sequence files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "tarfast5", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5", + "Galaxy wrapper version": "0.6.1", + "Conda id": "pigz", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "varscan_vaf", + "Galaxy tool ids": [ + "varscan_vaf" + ], + "Description": "Compute variant allele frequency in vcf files generated by varscan.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "varscan_vaf", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf", + "Galaxy wrapper version": "0.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "xpore", + "Galaxy tool ids": [ + "xpore_dataprep", + "xpore_diffmod" + ], + "Description": "Identification and quantification of differential RNA modifications from direct RNA sequencing", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/GoekeLab/xpore", + "ToolShed categories": [ + "Nanopore" + ], + "ToolShed id": "xpore", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore", + "Galaxy wrapper version": "2.1+galaxy0", + "Conda id": "xpore", + "Conda version": "2.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "yac_clipper", + "Galaxy tool ids": [ + "yac" + ], + "Description": "Clips 3' adapters for small RNA sequencing reads.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://artbio.fr", + "ToolShed categories": [ + "RNA", + "Fastq Manipulation" + ], + "ToolShed id": "yac_clipper", + "Galaxy wrapper owner": "artbio", + "Galaxy wrapper source": "https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper", + "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper", + "Galaxy wrapper version": "2.5.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "EMLassemblyline", + "Galaxy tool ids": [ + "eal_table_template", + "eal_templates", + "eml2eal", + "entities_template", + "geo_cov_template", + "makeeml", + "raster_template", + "taxo_cov_template", + "vector_template" + ], + "Description": "Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/EDIorg/EMLassemblyline", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "emlassemblyline", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline", + "Galaxy wrapper version": "0.1.1+galaxy0", + "Conda id": "r-emlassemblyline", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 9, + "Available on UseGalaxy.org.fr": 9 + }, + { + "Galaxy wrapper id": "Ecoregionalization_workflow", + "Galaxy tool ids": [ + "ecoregion_brt_analysis", + "ecoregion_GeoNearestNeighbor", + "ecoregion_cluster_estimate", + "ecoregion_clara_cluster", + "ecoregion_eco_map", + "ecoregion_taxa_seeker" + ], + "Description": "Tools to compute ecoregionalization with BRT model predictions and clustering.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/PaulineSGN/Workflow_Galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "ecoregionalization", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow", + "Galaxy wrapper version": "0.1.0+galaxy0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "Geom_mean_workflow", + "Galaxy tool ids": [ + "Map_shp", + "Mean_geom", + "bar_plot" + ], + "Description": "Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "Geometric means (Dead wood)", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow", + "Galaxy wrapper version": "0.1.0+galaxy0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "PAMPA", + "Galaxy tool ids": [ + "pampa_communitymetrics", + "pampa_presabs", + "pampa_glmcomm", + "pampa_glmsp", + "pampa_plotglm" + ], + "Description": "Tools to compute and analyse biodiversity metrics", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "pampa", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/ColineRoyaux/PAMPA-Galaxy", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA", + "Galaxy wrapper version": "0.0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 5, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "ab1_fastq", + "Galaxy tool ids": [ + "ab1_fastq_converter" + ], + "Description": "Tool to convert ab1 files into FASTQ files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "ab1fastq", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq", + "Galaxy wrapper version": "1.20.0", + "Conda id": "bioconductor-sangerseqr", + "Conda version": "1.38.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "aquainfra_importer", + "Galaxy tool ids": [ + "aquainfra_importer" + ], + "Description": "A data source tool for downloading datasets via the AquaINFRA Interaction Platform.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AquaINFRA/galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer", + "Galaxy wrapper version": "1.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "champ_blocs", + "Galaxy tool ids": [ + "cb_dissim", + "cb_ivr", + "cb_div" + ], + "Description": "Compute indicators for turnover boulders fields", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/Marie59/champ_blocs", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs", + "Galaxy wrapper version": "0.0.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 3 + }, + { + "Galaxy wrapper id": "consensus_from_alignments", + "Galaxy tool ids": [ + "aligned_to_consensus" + ], + "Description": "Tool to compute a consensus sequence from several aligned fasta sequences", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "consalign", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments", + "Galaxy wrapper version": "1.0.0", + "Conda id": "r-bioseq", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "data_exploration", + "Galaxy tool ids": [ + "tool_anonymization", + "ecology_homogeneity_normality", + "ecology_beta_diversity", + "ecology_link_between_var", + "ecology_presence_abs_abund", + "ecology_stat_presence_abs" + ], + "Description": "Explore data through multiple statistical tools", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/Marie59/Data_explo_tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration", + "Galaxy wrapper version": "0.0.0", + "Conda id": "r-tangles", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 6 + }, + { + "Galaxy wrapper id": "xarray", + "Galaxy tool ids": [ + "timeseries_extraction", + "xarray_coords_info", + "xarray_mapplot", + "xarray_metadata_info", + "xarray_netcdf2netcdf", + "xarray_select" + ], + "Description": "xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "http://xarray.pydata.org", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray", + "Galaxy wrapper version": "2022.3.0", + "Conda id": "xarray", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 5, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "gdal", + "Galaxy tool ids": [ + "gdal_gdal_merge", + "gdal_gdal_translate", + "gdal_gdaladdo", + "gdal_gdalbuildvrt", + "gdal_gdalinfo", + "gdal_gdalwarp", + "gdal_ogr2ogr", + "gdal_ogrinfo" + ], + "Description": "Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.gdal.org", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "gdal", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal", + "Galaxy wrapper version": "3.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 8 + }, + { + "Galaxy wrapper id": "interpolation", + "Galaxy tool ids": [ + "interpolation_run_idw_interpolation" + ], + "Description": "Run IDW interpolation based on a .csv and .geojson file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AquaINFRA/galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", + "Galaxy wrapper version": "1.0", + "Conda id": "r-getopt", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "medenv", + "Galaxy tool ids": [ + "iabiodiv_smartbiodiv_med_environ" + ], + "Description": "Retrieve environmental data from etopo, cmems and woa", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/jeremyfix/medenv", + "ToolShed categories": [ + "Ecology", + "Data Source" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/jeremyfix/medenv", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv", + "Galaxy wrapper version": "0.1.0", + "Conda id": "pandas", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "obisindicators", + "Galaxy tool ids": [ + "obisindicators", + "obis_data" + ], + "Description": "Compute biodiveristy indicators for marine data from obis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Marie59/obisindicators", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators", + "Galaxy wrapper version": "0.0.2", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "ocean", + "Galaxy tool ids": [ + "argo_getdata" + ], + "Description": "Access, process, visualise oceanographic data for the Earth System", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Marie59/FE-ft-ESG/tree/main/argo", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean", + "Galaxy wrapper version": "0.1.15", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ogcProcess_otb_bandmath", + "Galaxy tool ids": [ + "otb_band_math" + ], + "Description": "Outputs a monoband image which is the result of a mathematical operation on several multi-band images.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AquaINFRA/galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath", + "Galaxy wrapper version": "1.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ogcProcess_otb_meanShiftSmoothing", + "Galaxy tool ids": [ + "otb_mean_shift_smoothing" + ], + "Description": "This application smooths an image using the MeanShift algorithm.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AquaINFRA/galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing", + "Galaxy wrapper version": "1.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "regionalgam", + "Galaxy tool ids": [ + "regionalgam_ab_index", + "regionalgam_autocor_acf", + "regionalgam_flight_curve", + "regionalgam_glmmpql", + "regionalgam_gls_adjusted", + "regionalgam_gls", + "regionalgam_plot_trend" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RetoSchmucki/regionalGAM", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam", + "Galaxy wrapper version": "1.5", + "Conda id": "r-mgcv", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 7 + }, + { + "Galaxy wrapper id": "sdmpredictors", + "Galaxy tool ids": [ + "sdmpredictors_list_layers" + ], + "Description": "Terrestrial and marine predictors for species distribution modelling.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cran.r-project.org/web/packages/sdmpredictors/index.html", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "sdmpredictors", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors", + "Galaxy wrapper version": "0.2.15", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "spocc", + "Galaxy tool ids": [ + "spocc_occ" + ], + "Description": "Get species occurences data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cran.r-project.org/web/packages/spocc/index.html", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "spocc_occ", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc", + "Galaxy wrapper version": "1.2.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "srs_tools", + "Galaxy tool ids": [ + "srs_diversity_maps", + "srs_global_indices", + "srs_process_data", + "srs_spectral_indices", + "srs_pca", + "srs_preprocess_s2", + "srs_metadata" + ], + "Description": "Compute biodiversity indicators for remote sensing data from Sentinel 2", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/Marie59/Sentinel_2A/srs_tools", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools", + "Galaxy wrapper version": "0.0.1", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 7 + }, + { + "Galaxy wrapper id": "stoc", + "Galaxy tool ids": [ + "stoceps_filteringsp", + "stoceps_glm", + "stoceps_glm_group", + "stoceps_maketablecarrer", + "stoceps_trend_indic" + ], + "Description": "Tools to analyse STOC data.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "stoceps", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc", + "Galaxy wrapper version": "0.0.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 5 + }, + { + "Galaxy wrapper id": "vigiechiro", + "Galaxy tool ids": [ + "vigiechiro_bilanenrichipf", + "vigiechiro_bilanenrichirp", + "vigiechiro_idcorrect_2ndlayer", + "vigiechiro_idvalid" + ], + "Description": "Tools created by the vigiechiro team to analyses and identify chiro sounds files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": "vigiechiro", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro", + "Galaxy wrapper version": "0.1.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 4 + }, + { + "Galaxy wrapper id": "xmlstarlet", + "Galaxy tool ids": [ + "xmlstarlet" + ], + "Description": "Tool to convert a xml file from one metadata standard to another", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "xmlstarlet", + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet", + "Galaxy wrapper version": "1.6.1", + "Conda id": "xmlstarlet", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "zoo_project_ogc_api_processes", + "Galaxy tool ids": [ + "zoo_project_ogc_api_processes" + ], + "Description": "This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/AquaINFRA/galaxy", + "ToolShed categories": [ + "Ecology" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "ecology", + "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper", + "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes", + "Galaxy wrapper version": "0.1.0", + "Conda id": "r-base", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "c3s", + "Galaxy tool ids": [ + "c3s" + ], + "Description": "Copernicus Climate Change Service (C3S)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "c3s", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cads", + "Galaxy tool ids": [ + "cads" + ], + "Description": "Copernicus Atmosphere Data Store (ADS)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://ads.atmosphere.copernicus.eu/#!/home", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "cads", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads", + "Galaxy wrapper version": "0.1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cdo", + "Galaxy tool ids": [ + "cdo_info", + "cdo_operations" + ], + "Description": "CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://code.mpimet.mpg.de/projects/cdo/", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo", + "Galaxy wrapper version": "2.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cesm", + "Galaxy tool ids": [ + "cesm" + ], + "Description": "Community Earth System Model (CESM)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://www.cesm.ucar.edu/", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "cesm", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/ESCOMP/CESM", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm", + "Galaxy wrapper version": "2.1.3", + "Conda id": "cesm", + "Conda version": "2.1.3", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "climate-stripes", + "Galaxy tool ids": [ + "climate_stripes" + ], + "Description": "Create climate stripes from a tabular input file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://www.climate-lab-book.ac.uk/2018/warming-stripes/", + "ToolShed categories": [ + "Climate Analysis", + "Visualization" + ], + "ToolShed id": "climate_stripes", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes", + "Galaxy wrapper version": "1.0.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "eodie", + "Galaxy tool ids": [ + "eodie" + ], + "Description": "Earth Observation Data Information Extractor", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://eodie.readthedocs.io/", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "eodie", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://gitlab.com/eetun-tiimi/EODIE", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie", + "Galaxy wrapper version": "1.0.2", + "Conda id": "eodie", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "essential_climate_variables", + "Galaxy tool ids": [ + "cds_essential_variability" + ], + "Description": "Get Copernicus Essential Climate Variables for assessing climate variability", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview", + "ToolShed categories": [ + "Climate Analysis", + "Data Source" + ], + "ToolShed id": "cds_essential_variability", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fates-emerald", + "Galaxy tool ids": [ + "ctsm_fates" + ], + "Description": "EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "ctsm_fates", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald", + "Galaxy wrapper version": "2.0", + "Conda id": "fates-emerald", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mean-per-zone", + "Galaxy tool ids": [ + "mean_per_zone" + ], + "Description": "Creates a png image showing statistic over areas as defined in the vector file", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/", + "ToolShed categories": [ + "Visualization", + "GIS", + "Climate Analysis" + ], + "ToolShed id": "mean_per_zone", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone", + "Galaxy wrapper version": "0.2.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "psy-maps", + "Galaxy tool ids": [ + "psy_maps" + ], + "Description": "Visualization of regular geographical data on a map with psyplot", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/Chilipp/psy-maps", + "ToolShed categories": [ + "Visualization", + "Climate Analysis" + ], + "ToolShed id": "psy_maps", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps", + "Galaxy wrapper version": "1.2.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "shift-longitudes", + "Galaxy tool ids": [ + "shyft_longitudes" + ], + "Description": "Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/", + "ToolShed categories": [ + "Climate Analysis" + ], + "ToolShed id": "shift_longitudes", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes", + "Galaxy wrapper version": "0.1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "smithsonian-volcanoes", + "Galaxy tool ids": [ + "smithsonian_volcanoes" + ], + "Description": "Retrieve data from Volcanoes of the World (VOTW) Database", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://volcano.si.edu/gvp_votw.cfm", + "ToolShed categories": [ + "Retrieve Data" + ], + "ToolShed id": "smithsonian_volcanoes", + "Galaxy wrapper owner": "climate", + "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes", + "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes", + "Galaxy wrapper version": "0.1.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "droplet-barcode-plot", + "Galaxy tool ids": [ + "_dropletBarcodePlot" + ], + "Description": "Make a cell barcode plot for droplet single-cell RNA-seq QC", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "droplet_barcode_plot", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot", + "Galaxy wrapper version": "1.6.1+galaxy2", + "Conda id": "scxa-plots", + "Conda version": "0.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fastq_provider", + "Galaxy tool ids": [ + "fastq_provider" + ], + "Description": "Retrieval and download of FASTQ files from ENA and other repositories such as HCA.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ebi-gene-expression-group/atlas-fastq-provider", + "ToolShed categories": [ + "Data Source", + "RNA", + "Transcriptomics" + ], + "ToolShed id": "atlas_fastq_provider", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider", + "Galaxy wrapper version": "0.4.4", + "Conda id": "atlas-fastq-provider", + "Conda version": "0.4.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gtf-2-gene-list", + "Galaxy tool ids": [ + "_ensembl_gtf2gene_list" + ], + "Description": "Utility to extract annotations from Ensembl GTF files.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "gtf2gene_list", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list", + "Galaxy wrapper version": "1.52.0+galaxy0", + "Conda id": "atlas-gene-annotation-manipulation", + "Conda version": "1.1.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fastq_pair", + "Galaxy tool ids": [ + "fastq_pair" + ], + "Description": "Paired-end fastq pairer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/linsalrob/fastq-pair", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_pair", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair", + "Galaxy wrapper version": "1.0+galaxy0", + "Conda id": "fastq-pair", + "Conda version": "1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fastq_quality_trimmer", + "Galaxy tool ids": [ + "cshl_fastq_quality_trimmer" + ], + "Description": "FASTQ trimmer based on quality", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/agordon/fastx_toolkit", + "ToolShed categories": [ + "Fastq Manipulation" + ], + "ToolShed id": "fastq_quality_trimmer", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer", + "Galaxy wrapper version": "0.0.14+galaxy0", + "Conda id": "fastx_toolkit", + "Conda version": "0.0.14", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fastq_utils", + "Galaxy tool ids": [ + "fastq_filter_n", + "fastq_trim_poly_at" + ], + "Description": "Set of tools for handling fastq files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/nunofonseca/fastq_utils", + "ToolShed categories": [ + "Transcriptomics", + "RNA" + ], + "ToolShed id": "fastq_utils", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils", + "Galaxy wrapper version": "0.25.1+galaxy0", + "Conda id": "fastq_utils", + "Conda version": "0.25.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "salmon-kallisto-mtx-to-10x", + "Galaxy tool ids": [ + "_salmon_kallisto_mtx_to_10x" + ], + "Description": "Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "salmon_kallisto_mtx_to_10x", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x", + "Galaxy wrapper version": "0.0.1+galaxy6", + "Conda id": "scipy", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cell-types-analysis", + "Galaxy tool ids": [ + "ct_build_cell_ontology_dict", + "ct_check_labels", + "ct_combine_tool_outputs", + "ct_downsample_cells", + "ct_get_consensus_outputs", + "ct_get_empirical_dist", + "ct_get_tool_perf_table", + "ct_get_tool_pvals" + ], + "Description": "Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics" + ], + "ToolShed id": "suite_cell_types_analysis", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis", + "Galaxy wrapper version": "1.1.1", + "Conda id": "cell-types-analysis", + "Conda version": "0.1.11", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "data-hca", + "Galaxy tool ids": [ + "hca_matrix_downloader" + ], + "Description": "Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "suite_human_cell_atlas_tools", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca", + "Galaxy wrapper version": "v0.0.4+galaxy0", + "Conda id": "hca-matrix-downloader", + "Conda version": "0.0.4", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "data-scxa", + "Galaxy tool ids": [ + "retrieve_scxa" + ], + "Description": "Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis" + ], + "ToolShed id": "suite_ebi_expression_atlas", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa", + "Galaxy wrapper version": "v0.0.2+galaxy2", + "Conda id": "wget", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "decoupler", + "Galaxy tool ids": [ + "score_genes_aucell", + "decoupler_pathway_inference", + "decoupler_pseudobulk" + ], + "Description": "decoupler - Ensemble of methods to infer biological activities", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://decoupler-py.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "suite_decoupler", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler", + "Galaxy wrapper version": "1.4.0+galaxy3", + "Conda id": "decoupler", + "Conda version": "1.5.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "dropletutils", + "Galaxy tool ids": [ + "dropletutils_empty_drops", + "dropletutils_read_10x" + ], + "Description": "De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_dropletutils", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils", + "Galaxy wrapper version": "1.0.4", + "Conda id": "dropletutils-scripts", + "Conda version": "0.0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "garnett", + "Galaxy tool ids": [ + "garnett_check_markers", + "garnett_classify_cells", + "garnett_get_feature_genes", + "garnett_get_std_output", + "garnett_train_classifier", + "garnett_transform_markers", + "update_marker_file" + ], + "Description": "De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_garnett", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett", + "Galaxy wrapper version": "0.2.8", + "Conda id": "garnett-cli", + "Conda version": "0.0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "monocle3", + "Galaxy tool ids": [ + "monocle3_create", + "monocle3_diffExp", + "monocle3_learnGraph", + "monocle3_orderCells", + "monocle3_partition", + "monocle3_plotCells", + "monocle3_preprocess", + "monocle3_reduceDim", + "monocle3_topmarkers" + ], + "Description": "De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_monocle3", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3", + "Galaxy wrapper version": "0.1.4", + "Conda id": "monocle3-cli", + "Conda version": "0.0.9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 9, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 9, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sc3", + "Galaxy tool ids": [ + "sc3_calc_biology", + "sc3_calc_consens", + "sc3_calc_dists", + "sc3_calc_transfs", + "sc3_estimate_k", + "sc3_kmeans", + "sc3_prepare" + ], + "Description": "De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_sc3", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3", + "Galaxy wrapper version": "1.8.0", + "Conda id": "sc3-scripts", + "Conda version": "0.0.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scanpy", + "Galaxy tool ids": [ + "anndata_ops", + "scanpy_filter_cells", + "scanpy_filter_genes", + "scanpy_find_cluster", + "scanpy_find_markers", + "scanpy_find_variable_genes", + "scanpy_integrate_bbknn", + "scanpy_integrate_combat", + "scanpy_integrate_harmony", + "scanpy_integrate_mnn", + "scanpy_plot_scrublet", + "scanpy_multiplet_scrublet", + "scanpy_compute_graph", + "scanpy_normalise_data", + "scanpy_parameter_iterator", + "scanpy_plot_embed", + "scanpy_plot_trajectory", + "scanpy_read_10x", + "scanpy_regress_variable", + "scanpy_run_diffmap", + "scanpy_run_dpt", + "scanpy_run_fdg", + "scanpy_run_paga", + "scanpy_run_pca", + "scanpy_run_tsne", + "scanpy_run_umap", + "scanpy_scale_data" + ], + "Description": "scanpy-scripts, command-line wrapper scripts around Scanpy.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://scanpy.readthedocs.io", + "ToolShed categories": [ + "Transcriptomics", + "Sequence Analysis", + "RNA" + ], + "ToolShed id": "scanpy_scripts", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy", + "Galaxy wrapper version": "1.9.3", + "Conda id": "scanpy-scripts", + "Conda version": "1.9.301", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 17, + "Available on UseGalaxy.org.au": 27, + "Available on UseGalaxy.eu": 27, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scater", + "Galaxy tool ids": [ + "scater_calculate_cpm", + "scater_calculate_qc_metrics", + "scater_filter", + "scater_is_outlier", + "scater_normalize", + "scater_read_10x_results" + ], + "Description": "De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_scater", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater", + "Galaxy wrapper version": "1.10.0", + "Conda id": "scater-scripts", + "Conda version": "0.0.5", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 6, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sccaf", + "Galaxy tool ids": [ + "run_sccaf", + "sccaf_asses", + "sccaf_asses_merger", + "sccaf_regress_out" + ], + "Description": "SCCAF: Single Cell Clustering Assessment Framework.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/sccaf/sccaf", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "SCCAF", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf", + "Galaxy wrapper version": "0.0.9", + "Conda id": "sccaf", + "Conda version": "0.0.10", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "sceasy", + "Galaxy tool ids": [ + "sceasy_convert" + ], + "Description": "Convert scRNA data object between popular formats", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "sceasy", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy", + "Galaxy wrapper version": "0.0.5", + "Conda id": "r-sceasy", + "Conda version": "0.0.7", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scmap", + "Galaxy tool ids": [ + "scmap_get_std_output", + "scmap_index_cell", + "scmap_index_cluster", + "scmap_preprocess_sce", + "scmap_scmap_cell", + "scmap_scmap_cluster", + "scmap_select_features" + ], + "Description": "De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_scmap", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap", + "Galaxy wrapper version": "1.6.4", + "Conda id": "scmap-cli", + "Conda version": "0.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 7, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "scpred", + "Galaxy tool ids": [ + "scpred_get_feature_space", + "scpred_get_std_output", + "scpred_predict_labels", + "scpred_train_model" + ], + "Description": "De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_scpred", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred", + "Galaxy wrapper version": "1.0.2", + "Conda id": "scpred-cli", + "Conda version": "0.1.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 4, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "seurat", + "Galaxy tool ids": [ + "seurat_convert", + "seurat_dim_plot", + "seurat_export_cellbrowser", + "seurat_filter_cells", + "seurat_find_clusters", + "seurat_find_markers", + "seurat_find_neighbours", + "seurat_find_variable_genes", + "seurat_hover_locator", + "seurat_integration", + "seurat_map_query", + "seurat_normalise_data", + "seurat_plot", + "seurat_read10x", + "seurat_run_pca", + "seurat_run_tsne", + "seurat_run_umap", + "seurat_scale_data", + "seurat_select_integration_features" + ], + "Description": "De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/", + "ToolShed categories": [ + "Transcriptomics", + "RNA", + "Statistics", + "Sequence Analysis" + ], + "ToolShed id": "suite_seurat", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat", + "Galaxy wrapper version": "4.0.0", + "Conda id": "seurat-scripts", + "Conda version": "4.0.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 14, + "Available on UseGalaxy.org.fr": 11 + }, + { + "Galaxy wrapper id": "ucsc-cell-browser", + "Galaxy tool ids": [ + "ucsc_cell_browser" + ], + "Description": "Python pipeline and Javascript scatter plot library for single-cell datasets", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://cells.ucsc.edu/", + "ToolShed categories": [ + "Transcriptomics" + ], + "ToolShed id": "ucsc_cell_browser", + "Galaxy wrapper owner": "ebi-gxa", + "Galaxy wrapper source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml", + "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser", + "Galaxy wrapper version": "1.0.0+galaxy1", + "Conda id": "ucsc-cell-browser", + "Conda version": "1.2.6", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "biotransformer", + "Galaxy tool ids": [ + "biotransformer" + ], + "Description": "BioTransformer is a tool for prediction of small molecule metabolism in mammals.", + "bio.tool id": "biotransformer", + "bio.tool ids": [ + "biotransformer" + ], + "biii": null, + "bio.tool name": "BioTransformer", + "bio.tool description": "BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.", + "EDAM operation": [ + "Metabolic pathway prediction", + "PTM site prediction", + "Natural product identification" + ], + "EDAM topic": [ + "Small molecules", + "Endocrinology and metabolism", + "Metabolomics", + "Carbohydrates", + "NMR" + ], + "Status": "Up-to-date", + "Source": "https://bitbucket.org/djoumbou/biotransformerjar/src/master/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "biotransformer", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer", + "Galaxy wrapper version": "3.0.20230403", + "Conda id": "biotransformer", + "Conda version": "3.0.20230403", + "EDAM operation (no superclasses)": [ + "Metabolic pathway prediction", + "PTM site prediction", + "Natural product identification" + ], + "EDAM topic (no superclasses)": [ + "Small molecules", + "Endocrinology and metabolism", + "Metabolomics", + "Carbohydrates", + "NMR" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "filter_compounds", + "Galaxy tool ids": [ + "filter_orgmet_anorg" + ], + "Description": "Tool for filtering organometallics/anorganic compounds from a list of compounds.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "filter_compounds", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds", + "Galaxy wrapper version": "3.1.1", + "Conda id": "openbabel", + "Conda version": "2.3.90dev7d621d9", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "gc_derivatization", + "Galaxy tool ids": [ + "gc_derivatization" + ], + "Description": "In silico derivatization for GC.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/gc-meox-tms", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "gc_derivatization", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization", + "Galaxy wrapper version": "1.0.1", + "Conda id": "gc-meox-tms", + "Conda version": "1.0.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "isolib", + "Galaxy tool ids": [ + "isolib" + ], + "Description": "Create an isotopic pattern library for given compounds and adducts.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "isolib", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/isolib", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/isolib", + "Galaxy wrapper version": "1.0.1+galaxy0", + "Conda id": "bioconductor-metabocoreutils", + "Conda version": "1.10.0", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "matchms", + "Galaxy tool ids": [ + "matchms_add_key", + "matchms_convert", + "matchms_filtering", + "matchms_fingerprint_similarity", + "matchms_formatter", + "matchms_metadata_export", + "matchms_metadata_match", + "matchms_metadata_merge", + "matchms_networking", + "matchms_remove_key", + "matchms_remove_spectra", + "matchms_spectral_similarity", + "matchms_split", + "matchms_subsetting" + ], + "Description": "Searching, filtering and converting mass spectral libraries.", + "bio.tool id": "matchms", + "bio.tool ids": [ + "matchms" + ], + "biii": null, + "bio.tool name": "Matchms", + "bio.tool description": "Tool to import, process, clean, and compare mass spectrometry data.", + "EDAM operation": [ + "Spectral library search", + "Format validation", + "Filtering" + ], + "EDAM topic": [ + "Metabolomics" + ], + "Status": "To update", + "Source": "https://github.com/matchms/matchms", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "matchms", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/matchms", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/matchms", + "Galaxy wrapper version": "0.25.0", + "Conda id": "matchms", + "Conda version": "0.26.2", + "EDAM operation (no superclasses)": [ + "Spectral library search", + "Format validation", + "Filtering" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 9, + "Available on UseGalaxy.eu": 14, + "Available on UseGalaxy.org.fr": 11 + }, + { + "Galaxy wrapper id": "misc", + "Galaxy tool ids": [ + "use_theoretical_mz_annotations" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc", + "Galaxy wrapper version": "1.0.0", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "msmetaenhancer", + "Galaxy tool ids": [ + "msmetaenhancer" + ], + "Description": null, + "bio.tool id": "msmetaenhancer", + "bio.tool ids": [ + "msmetaenhancer" + ], + "biii": null, + "bio.tool name": "MSMetaEnhancer", + "bio.tool description": "Tool for mass spectra metadata annotation.", + "EDAM operation": [ + "Annotation", + "Standardisation and normalisation" + ], + "EDAM topic": [ + "Metabolomics", + "Compound libraries and screening", + "Data submission, annotation and curation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/MSMetaEnhancer", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer", + "Galaxy wrapper version": "0.4.0", + "Conda id": "msmetaenhancer", + "Conda version": "0.4.0", + "EDAM operation (no superclasses)": [ + "Annotation", + "Standardisation and normalisation" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics", + "Compound libraries and screening", + "Data submission, annotation and curation" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "msp_merge", + "Galaxy tool ids": [ + "msp_merge" + ], + "Description": null, + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge", + "Galaxy wrapper version": "0.1.0", + "Conda id": "matchms", + "Conda version": "0.26.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "mzml_validator", + "Galaxy tool ids": [ + "mzml_validator" + ], + "Description": "mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools", + "ToolShed categories": [ + "Metabolomics", + "Proteomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator", + "Galaxy wrapper version": "0.1.0+galaxy2", + "Conda id": "lxml", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "qcxms", + "Galaxy tool ids": [ + "qcxms_getres", + "qcxms_neutral_run", + "qcxms_production_run" + ], + "Description": "QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/grimme-lab/QCxMS", + "ToolShed categories": [ + "Computational chemistry", + "Molecular Dynamics" + ], + "ToolShed id": "QCxMS", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms", + "Galaxy wrapper version": "5.2.1", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 3, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "query", + "Galaxy tool ids": [ + "query" + ], + "Description": "Execute an SQL statement on a set of tables", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Text Manipulation" + ], + "ToolShed id": "query", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/query", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/query", + "Galaxy wrapper version": "0.2", + "Conda id": "click", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ramclustr", + "Galaxy tool ids": [ + "ramclustr", + "ramclustr_define_experiment" + ], + "Description": null, + "bio.tool id": "ramclustr", + "bio.tool ids": [ + "ramclustr" + ], + "biii": null, + "bio.tool name": "RAMClustR", + "bio.tool description": "A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.", + "EDAM operation": [ + "Imputation", + "Standardisation and normalisation", + "Clustering", + "Correlation" + ], + "EDAM topic": [ + "Metabolomics" + ], + "Status": "To update", + "Source": "https://rdrr.io/cran/RAMClustR/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr", + "Galaxy wrapper version": "1.3.0", + "Conda id": "r-ramclustr", + "Conda version": "1.3.1", + "EDAM operation (no superclasses)": [ + "Imputation", + "Standardisation and normalisation", + "Clustering", + "Correlation" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics" + ], + "Available on UseGalaxy.org": 2, + "Available on UseGalaxy.org.au": 2, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 2 + }, + { + "Galaxy wrapper id": "recetox_aplcms", + "Galaxy tool ids": [ + "recetox_aplcms_align_features", + "recetox_aplcms_compute_clusters", + "recetox_aplcms_compute_template", + "recetox_aplcms_correct_time", + "recetox_aplcms_generate_feature_table", + "recetox_aplcms_merge_known_table", + "recetox_aplcms_recover_weaker_signals", + "recetox_aplcms_remove_noise" + ], + "Description": "Peak detection tool for HRMS profile data.", + "bio.tool id": "recetox-aplcms", + "bio.tool ids": [ + "recetox-aplcms" + ], + "biii": null, + "bio.tool name": "recetox-aplcms", + "bio.tool description": "recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.", + "EDAM operation": [ + "Chromatographic alignment", + "Quantification", + "Peak detection", + "Feature extraction", + "Alignment" + ], + "EDAM topic": [ + "Metabolomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/recetox-aplcms", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "recetox-aplcms", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms", + "Galaxy wrapper version": "0.12.0", + "Conda id": "r-recetox-aplcms", + "Conda version": "0.12.0", + "EDAM operation (no superclasses)": [ + "Chromatographic alignment", + "Quantification", + "Peak detection", + "Feature extraction", + "Alignment" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 8, + "Available on UseGalaxy.eu": 8, + "Available on UseGalaxy.org.fr": 8 + }, + { + "Galaxy wrapper id": "recetox_msfinder", + "Galaxy tool ids": [ + "recetox_msfinder" + ], + "Description": null, + "bio.tool id": "recetox-msfinder", + "bio.tool ids": [ + "recetox-msfinder" + ], + "biii": null, + "bio.tool name": "recetox-msfinder", + "bio.tool description": "This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.", + "EDAM operation": [ + "Annotation" + ], + "EDAM topic": [ + "Metabolomics" + ], + "Status": "To update", + "Source": "https://github.com/RECETOX/recetox-msfinder", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder", + "Galaxy wrapper version": "v3.5.2", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Annotation" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "recetox_xmsannotator", + "Galaxy tool ids": [ + "recetox_xmsannotator_advanced" + ], + "Description": null, + "bio.tool id": "recetox-xmsannotator", + "bio.tool ids": [ + "recetox-xmsannotator" + ], + "biii": null, + "bio.tool name": "recetox-xMSannotator", + "bio.tool description": "Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.", + "EDAM operation": [ + "Expression profile pathway mapping", + "Structure comparison", + "Isotopic distributions calculation", + "Annotation" + ], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/recetox-xMSannotator", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator", + "Galaxy wrapper version": "0.10.0", + "Conda id": "r-recetox-xmsannotator", + "Conda version": "0.10.0", + "EDAM operation (no superclasses)": [ + "Expression profile pathway mapping", + "Structure comparison", + "Isotopic distributions calculation", + "Annotation" + ], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rem_complex", + "Galaxy tool ids": [ + "rem_complex" + ], + "Description": "Removes molecular coordination complexes.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "rem_complex", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex", + "Galaxy wrapper version": "1.0.0", + "Conda id": "pandas", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "rename_annotated_feature", + "Galaxy tool ids": [ + "rename_annotated_feature" + ], + "Description": "Update column names in an abundance table using a annotation table with spectral matching results", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/RECETOX/galaxytools/", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "rename_annotated_feature", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature", + "Galaxy wrapper version": "1.0.0", + "Conda id": "pandas", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "retip", + "Galaxy tool ids": [ + "retip_apply", + "retip_descriptors", + "retip_filter_rt", + "retip_train" + ], + "Description": null, + "bio.tool id": "retip", + "bio.tool ids": [ + "retip" + ], + "biii": null, + "bio.tool name": "Retip", + "bio.tool description": "Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.", + "EDAM operation": [ + "Retention time prediction", + "Spectrum calculation", + "Deisotoping", + "Formatting", + "Deposition" + ], + "EDAM topic": [ + "Metabolomics", + "Proteomics experiment", + "Machine learning", + "Cheminformatics", + "Chemistry" + ], + "Status": "To update", + "Source": "https://github.com/PaoloBnn/Retip", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/retip", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/retip", + "Galaxy wrapper version": "0.5.4", + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [ + "Retention time prediction", + "Spectrum calculation", + "Deisotoping", + "Formatting", + "Deposition" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics", + "Proteomics experiment", + "Machine learning", + "Cheminformatics", + "Chemistry" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "riassigner", + "Galaxy tool ids": [ + "riassigner", + "riassigner_from_comment" + ], + "Description": null, + "bio.tool id": "riassigner", + "bio.tool ids": [ + "riassigner" + ], + "biii": null, + "bio.tool name": "RIAssigner", + "bio.tool description": "RIAssigner is a python tool for retention index (RI) computation for GC-MS data.", + "EDAM operation": [ + "Standardisation and normalisation" + ], + "EDAM topic": [ + "Metabolomics", + "Compound libraries and screening", + "Data submission, annotation and curation" + ], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/RIAssigner", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner", + "Galaxy wrapper version": "0.4.1", + "Conda id": "riassigner", + "Conda version": "0.4.1", + "EDAM operation (no superclasses)": [ + "Standardisation and normalisation" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics", + "Compound libraries and screening", + "Data submission, annotation and curation" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 2, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "rmassbank", + "Galaxy tool ids": [ + "rmassbank" + ], + "Description": "RMassBank is an R package for processing tandem MS files and building of MassBank records.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/MassBank/RMassBank", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "rmassbank", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank", + "Galaxy wrapper version": "3.0.0", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 1, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "spec2vec", + "Galaxy tool ids": [ + "spec2vec_similarity", + "spec2vec_training" + ], + "Description": "Mass spectra similarity scoring using a trained Spec2Vec model.", + "bio.tool id": "spec2vec", + "bio.tool ids": [ + "spec2vec" + ], + "biii": null, + "bio.tool name": "Spec2Vec", + "bio.tool description": "Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.", + "EDAM operation": [ + "Spectrum calculation", + "Spectral library search", + "Database search", + "Natural product identification" + ], + "EDAM topic": [ + "Proteomics experiment", + "Metabolomics", + "Natural language processing", + "Proteomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/iomega/spec2vec", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "spec2vec", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec", + "Galaxy wrapper version": "0.8.0", + "Conda id": "spec2vec", + "Conda version": "0.8.0", + "EDAM operation (no superclasses)": [ + "Spectrum calculation", + "Spectral library search", + "Database search", + "Natural product identification" + ], + "EDAM topic (no superclasses)": [ + "Proteomics experiment", + "Metabolomics", + "Natural language processing", + "Proteomics" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "waveica", + "Galaxy tool ids": [ + "waveica" + ], + "Description": "Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.", + "bio.tool id": "waveica", + "bio.tool ids": [ + "waveica" + ], + "biii": null, + "bio.tool name": "WaveICA", + "bio.tool description": "Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.", + "EDAM operation": [ + "Standardisation and normalisation" + ], + "EDAM topic": [ + "Metabolomics" + ], + "Status": "Up-to-date", + "Source": "https://github.com/RECETOX/WaveICA", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": null, + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/waveica", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/waveica", + "Galaxy wrapper version": "0.2.0", + "Conda id": "r-recetox-waveica", + "Conda version": "0.2.0", + "EDAM operation (no superclasses)": [ + "Standardisation and normalisation" + ], + "EDAM topic (no superclasses)": [ + "Metabolomics" + ], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "xtb", + "Galaxy tool ids": [ + "xtb_molecular_optimization" + ], + "Description": "Performs semiempirical molecular optimization.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/grimme-lab/xtb", + "ToolShed categories": [ + "Metabolomics" + ], + "ToolShed id": "xtb_molecular_optimization", + "Galaxy wrapper owner": "recetox", + "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/xtb", + "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/xtb", + "Galaxy wrapper version": "6.6.1", + "Conda id": "xtb", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 1 + }, + { + "Galaxy wrapper id": "consolidate_vcfs", + "Galaxy tool ids": [ + "consolidate_vcfs" + ], + "Description": "Combines freebayes and mpileup files for use by vcf2snvalignment", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "consolidate_vcfs", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "filter_density", + "Galaxy tool ids": [ + "filterdensity" + ], + "Description": "Filter out position based on distance between SNVs", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "filter_density", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "filter_stats", + "Galaxy tool ids": [ + "filterstat" + ], + "Description": "SNVPhyl filter_stats", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "filter_stats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "filter_vcf", + "Galaxy tool ids": [ + "filtervcf" + ], + "Description": "SNVPhyl filter_vcf", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "filter_vcf", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "find_repeats", + "Galaxy tool ids": [ + "findrepeat" + ], + "Description": "Find repetitive regions on a reference genome using MUMMer", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "find_repeats", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "positions2snv_alignment", + "Galaxy tool ids": [ + "positions2snv_alignment" + ], + "Description": "Generate alignment of SNVs from SNVPhyl variant table.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "positions2snv_alignment", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "positions2snv_invariant_alignment", + "Galaxy tool ids": [ + "positions2snv_invariant_alignment" + ], + "Description": "Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Variant Analysis" + ], + "ToolShed id": "positions2snv_invariant_alignment", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "snv_matrix", + "Galaxy tool ids": [ + "snvmatrix" + ], + "Description": "Generate matrix of SNV distances", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "snv_matrix", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "vcf2snvalignment", + "Galaxy tool ids": [ + "vcf2snvalignment" + ], + "Description": "Generates multiple alignment of variant calls", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "vcf2snvalignment", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "verify_map", + "Galaxy tool ids": [ + "verify_map" + ], + "Description": "Checks the mapping quality of all BAM(s)", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "Up-to-date", + "Source": "https://snvphyl.readthedocs.io/en/latest/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "verify_map", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map", + "Galaxy wrapper version": "1.8.2", + "Conda id": "snvphyl-tools", + "Conda version": "1.8.2", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "suite_snvphyl", + "Galaxy tool ids": [], + "Description": "SNVPhyl suite defining all dependencies for SNVPhyl", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "suite_snvphyl_1_2_3", + "Galaxy wrapper owner": "nml", + "Galaxy wrapper source": "https://github.com/phac-nml/snvphyl-galaxy", + "Galaxy wrapper parsed folder": "https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl", + "Galaxy wrapper version": null, + "Conda id": null, + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "cooler", + "Galaxy tool ids": [ + "cooler_balance", + "cooler_cload_tabix", + "cooler_csort_tabix", + "cooler_makebins", + "cooler_zoomify" + ], + "Description": "cooler different tools to process Hi-C from mirnylab", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/open2c/cooler", + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "cooler", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler", + "Galaxy wrapper version": "0.9.3", + "Conda id": "htslib", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 4, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 5, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fromHicupToJuicebox", + "Galaxy tool ids": [ + "fromHicupToJuicebox" + ], + "Description": "Convert the output of hicup (as sam or bam) to the input of juicebox.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "from_hicup_to_juicebox", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox", + "Galaxy wrapper version": "0.0.2", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "fromgtfTobed12", + "Galaxy tool ids": [ + "fromgtfTobed12" + ], + "Description": "Convert GTF files to BED12 format", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://pythonhosted.org/gffutils/contents.html", + "ToolShed categories": [ + "Convert Formats" + ], + "ToolShed id": "fromgtftobed12", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12", + "Galaxy wrapper version": "0.11.1+galaxy1", + "Conda id": "gffutils", + "Conda version": "0.13", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "getTn5ExtendedCoverage", + "Galaxy tool ids": [ + "getTn5ExtendedCoverage" + ], + "Description": "Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Epigenetics" + ], + "ToolShed id": "gettn5extendedcoverage", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": null, + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage", + "Galaxy wrapper version": "0.0.2", + "Conda id": "pysam", + "Conda version": "0.22.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "hyperstack_to_bleach_corrected_movie", + "Galaxy tool ids": [ + "hyperstack_to_bleach_corrected_movie" + ], + "Description": "Generate blach corrected movie from hyperstack", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "hyperstack_to_bleach_corrected_movie", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie", + "Galaxy wrapper version": "20230328", + "Conda id": "Fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "incucyte_stack_and_upload_omero", + "Galaxy tool ids": [ + "incucyte_stack_and_upload_omero" + ], + "Description": "Combine images to stack and upload to the omero server", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "incucyte_stack_and_upload_omero", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero", + "Galaxy wrapper version": "20231221", + "Conda id": "Fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "measure_gastruloids", + "Galaxy tool ids": [ + "measureGastruloids" + ], + "Description": "Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "measure_gastruloids", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids", + "Galaxy wrapper version": "20221216", + "Conda id": "fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "omero_clean_rois_tables", + "Galaxy tool ids": [ + "omero_clean_rois_tables" + ], + "Description": "Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "omero_clean_rois_tables", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables", + "Galaxy wrapper version": "20230623", + "Conda id": "fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "omero_get_children_ids", + "Galaxy tool ids": [ + "omero_get_children_ids" + ], + "Description": "Get omero id of children of an omero object id", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "omero_get_children_ids", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids", + "Galaxy wrapper version": "0.1.0", + "Conda id": "omero-py", + "Conda version": "5.11.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "omero_get_full_images", + "Galaxy tool ids": [ + "omero_get_full_images" + ], + "Description": "Get full images from omero", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "omero_get_full_images", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images", + "Galaxy wrapper version": "20240521", + "Conda id": "fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "omero_hyperstack_to_fluo_measurements_on_gastruloid", + "Galaxy tool ids": [ + "omero_hyperstack_to_fluo_measurements_on_gastruloid" + ], + "Description": "Analyse Hyperstack on OMERO server to measure fluorescence levels", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "omero_hyperstack_to_fluo_measurements_on_gastruloid", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid", + "Galaxy wrapper version": "20230809", + "Conda id": "fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "omero_hyperstack_to_gastruloid_measurements", + "Galaxy tool ids": [ + "omero_hyperstack_to_gastruloid_measurements" + ], + "Description": "Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "omero_hyperstack_to_gastruloid_measurements", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements", + "Galaxy wrapper version": "20240214", + "Conda id": "fiji", + "Conda version": "20231211", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "revertR2orientationInBam", + "Galaxy tool ids": [ + "revertR2orientationInBam" + ], + "Description": "Revert the mapped orientation of R2 mates in a bam.", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "SAM" + ], + "ToolShed id": "revertr2orientationinbam", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam", + "Galaxy wrapper version": "0.0.2", + "Conda id": "samtools", + "Conda version": "1.20", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 1, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "upload_roi_and_measures_to_omero", + "Galaxy tool ids": [ + "uploadROIandMeasuresToOMERO" + ], + "Description": "Upload the ROI coordinates and the measurements to the omero server", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": null, + "ToolShed categories": [ + "Imaging" + ], + "ToolShed id": "upload_roi_and_measures_to_omero", + "Galaxy wrapper owner": "lldelisle", + "Galaxy wrapper source": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero", + "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero", + "Galaxy wrapper version": "0.0.5", + "Conda id": "omero-py", + "Conda version": "5.11.1", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast2go", + "Galaxy tool ids": [ + "blast2go" + ], + "Description": "Maps BLAST results to GO annotation terms", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", + "ToolShed categories": [ + "Ontology Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "blast2go", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go", + "Galaxy wrapper version": "0.0.11", + "Conda id": "b2g4pipe", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blast_rbh", + "Galaxy tool ids": [ + "blast_reciprocal_best_hits" + ], + "Description": "BLAST Reciprocal Best Hits (RBH) from two FASTA files", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "blast_rbh", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh", + "Galaxy wrapper version": "0.3.0", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "blastxml_to_top_descr", + "Galaxy tool ids": [ + "blastxml_to_top_descr" + ], + "Description": "Make table of top BLAST match descriptions", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", + "ToolShed categories": [ + "Convert Formats", + "Sequence Analysis", + "Text Manipulation" + ], + "ToolShed id": "blastxml_to_top_descr", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr", + "Galaxy wrapper version": "0.1.2", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 1, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "make_nr", + "Galaxy tool ids": [ + "make_nr" + ], + "Description": "Make a FASTA file non-redundant", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", + "ToolShed categories": [ + "Fasta Manipulation", + "Sequence Analysis" + ], + "ToolShed id": "make_nr", + "Galaxy wrapper owner": "peterjc", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr", + "Galaxy wrapper version": "0.0.2", + "Conda id": "biopython", + "Conda version": "1.70", + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 0 + }, + { + "Galaxy wrapper id": "ncbi_blast_plus", + "Galaxy tool ids": [ + "blastxml_to_tabular", + "get_species_taxids", + "ncbi_blastdbcmd_info", + "ncbi_blastdbcmd_wrapper", + "ncbi_blastn_wrapper", + "ncbi_blastp_wrapper", + "ncbi_blastx_wrapper", + "ncbi_convert2blastmask_wrapper", + "ncbi_deltablast_wrapper", + "ncbi_dustmasker_wrapper", + "ncbi_makeblastdb", + "ncbi_makeprofiledb", + "ncbi_psiblast_wrapper", + "ncbi_rpsblast_wrapper", + "ncbi_rpstblastn_wrapper", + "ncbi_segmasker_wrapper", + "ncbi_tblastn_wrapper", + "ncbi_tblastx_wrapper" + ], + "Description": "NCBI BLAST+", + "bio.tool id": null, + "bio.tool ids": [], + "biii": null, + "bio.tool name": null, + "bio.tool description": null, + "EDAM operation": [], + "EDAM topic": [], + "Status": "To update", + "Source": "https://blast.ncbi.nlm.nih.gov/", + "ToolShed categories": [ + "Sequence Analysis" + ], + "ToolShed id": "ncbi_blast_plus", + "Galaxy wrapper owner": "devteam", + "Galaxy wrapper source": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", + "Galaxy wrapper parsed folder": "https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus", + "Galaxy wrapper version": "2.14.1", + "Conda id": "python", + "Conda version": null, + "EDAM operation (no superclasses)": [], + "EDAM topic (no superclasses)": [], + "Available on UseGalaxy.org": 16, + "Available on UseGalaxy.org.au": 16, + "Available on UseGalaxy.eu": 16, + "Available on UseGalaxy.org.fr": 16 + }, + { + "Galaxy wrapper id": "frogs", + "Galaxy tool ids": [ + "FROGS_affiliation_filters", + "FROGS_affiliation_postprocess", + "FROGS_affiliation_stats", + "FROGS_biom_to_stdBiom", + "FROGS_biom_to_tsv", + "FROGS_cluster_filters", + "FROGS_cluster_stats", + "FROGS_clustering", + "FROGS_demultiplex", + "FROGSSTAT_DESeq2_Preprocess", + "FROGSSTAT_DESeq2_Visualisation", + "FROGSFUNC_step2_functions", + "FROGSFUNC_step3_pathways", + "FROGSFUNC_step1_placeseqs", + "FROGS_itsx", + "FROGS_normalisation", + "FROGSSTAT_Phyloseq_Alpha_Diversity", + "FROGSSTAT_Phyloseq_Beta_Diversity", + "FROGSSTAT_Phyloseq_Sample_Clustering", + "FROGSSTAT_Phyloseq_Composition_Visualisation", + "FROGSSTAT_Phyloseq_Import_Data", + "FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance", + "FROGSSTAT_Phyloseq_Structure_Visualisation", + "FROGS_preprocess", + "FROGS_remove_chimera", + "FROGS_taxonomic_affiliation", + "FROGS_Tree", + "FROGS_tsv_to_biom" + ], + "Description": "Suite for metabarcoding analysis", + "bio.tool id": "frogs", + "bio.tool ids": [ + "frogs" + ], + "biii": null, + "bio.tool name": "FROGS", + "bio.tool description": "The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.", + "EDAM operation": [ + "Taxonomic classification" + ], + "EDAM topic": [ + "Metagenomics", + "Microbial ecology", + "Taxonomy", + "Evolutionary biology", + "Sequencing" + ], + "Status": "Up-to-date", + "Source": "http://frogs.toulouse.inrae.fr/", + "ToolShed categories": [ + "Metagenomics" + ], + "ToolShed id": "frogs", + "Galaxy wrapper owner": "frogs", + "Galaxy wrapper source": "https://github.com/geraldinepascal/FROGS-wrappers/", + "Galaxy wrapper parsed folder": "https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs", + "Galaxy wrapper version": "4.1.0", + "Conda id": "frogs", + "Conda version": "4.1.0", + "EDAM operation (no superclasses)": [ + "Taxonomic classification" + ], + "EDAM topic (no superclasses)": [ + "Metagenomics", + "Microbial ecology", + "Taxonomy", + "Evolutionary biology", + "Sequencing" + ], + "Available on UseGalaxy.org": 0, + "Available on UseGalaxy.org.au": 0, + "Available on UseGalaxy.eu": 0, + "Available on UseGalaxy.org.fr": 28 + } ]