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Merge remote-tracking branch 'origin/galaxytool-import-branch'
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106 files changed

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‎data/amrfinderplus/amrfinderplus.galaxy.json‎

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"EDAM_reduced_topics": "Microbiology, Public health and epidemiology, Infectious disease",
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"EDAM_topics": "Microbiology, Public health and epidemiology, Infectious disease",
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"Homepage": "https://github.com/ncbi/amr",
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"Latest_suite_conda_package_version": "4.0.15",
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"Latest_suite_conda_package_version": "4.0.19",
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"Number_of_tools_on_UseGalaxy.eu": 1,
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"Number_of_tools_on_UseGalaxy.fr": 1,
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"Number_of_tools_on_UseGalaxy.org_(Main)": 1,

‎data/andersen-lab_ivar/andersen-lab_ivar.galaxy.json‎

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{
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"Description": "iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing",
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"EDAM_operations": "Primer removal",
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"EDAM_reduced_operations": "Primer removal",
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"EDAM_reduced_topics": "Virology",
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"EDAM_topics": "Virology",
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"Homepage": "https://github.com/andersen-lab/ivar",
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"Latest_suite_conda_package_version": "1.4.3",
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"Number_of_tools_on_GalaxyTrakr": 5,
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"Number_of_tools_on_MISSISSIPPI": 4,
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"Number_of_tools_on_UseGalaxy.be": 5,
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"Number_of_tools_on_UseGalaxy.cz": 5,
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"Number_of_tools_on_UseGalaxy.eu": 5,
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"Number_of_tools_on_UseGalaxy.fr": 5,
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"Number_of_tools_on_UseGalaxy.no": 5,
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"Number_of_tools_on_UseGalaxy.org.au": 5,
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"Number_of_tools_on_UseGalaxy.org_(Main)": 5,
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"Suite_ID": "ivar",
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"Suite_conda_package": "ivar",
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"Suite_first_commit_date": "2020-03-21",
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"Suite_owner": "iuc",
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"Suite_parsed_folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar",
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"Suite_runs_(last_5_years)_(usegalaxy.eu)": 1252220,
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"Suite_runs_(last_5_years)_(usegalaxy.org)": 126027,
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"Suite_runs_(last_5_years)_(usegalaxy.org.au)": 41901,
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"Suite_runs_(last_5_years)_on_main_servers": 1420148,
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"Suite_runs_(usegalaxy.eu)": 1252220,
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"Suite_runs_(usegalaxy.org)": 126027,
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"Suite_runs_(usegalaxy.org.au)": 41901,
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"Suite_runs_on_main_servers": 4260444,
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"Suite_source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/",
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"Suite_users_(last_5_years)_(usegalaxy.eu)": 2366,
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"Suite_users_(last_5_years)_(usegalaxy.org)": 2496,
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"Suite_users_(last_5_years)_(usegalaxy.org.au)": 993,
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"Suite_users_(last_5_years)_on_main_servers": 5855,
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"Suite_users_(usegalaxy.eu)": 2366,
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"Suite_users_(usegalaxy.org)": 2496,
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"Suite_users_(usegalaxy.org.au)": 993,
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"Suite_users_on_main_servers": 17565,
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"Suite_version": "1.4.3",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Sequence Analysis",
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"Tool_IDs": "ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants",
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"bio.tool_ID": "andersen-lab_ivar",
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"bio.tool_description": "iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.",
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"bio.tool_name": "iVar"
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}

‎data/bbmap/bbmap.galaxy.json‎

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"Latest_suite_conda_package_version": "39.15",
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"Number_of_tools_on_GalaxyTrakr": 3,
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"Number_of_tools_on_UseGalaxy.cz": 4,
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"Number_of_tools_on_UseGalaxy.eu": 5,
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"Number_of_tools_on_UseGalaxy.eu": 6,
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"Number_of_tools_on_UseGalaxy.fr": 6,
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"Number_of_tools_on_UseGalaxy.org.au": 3,
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"Number_of_tools_on_UseGalaxy.org_(Main)": 6,

‎data/cami-amber/cami-amber.galaxy.json‎

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{
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"Description": "Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments",
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"EDAM_operations": "Read binning",
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"EDAM_reduced_operations": "Read binning",
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"EDAM_reduced_topics": "Metagenomics",
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"EDAM_topics": "Metagenomics",
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"Homepage": "https://github.com/CAMI-challenge/AMBER",
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"Latest_suite_conda_package_version": "2.0.7",
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"Number_of_tools_on_UseGalaxy.eu": 4,
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"Suite_ID": "cami_amber",
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"Suite_conda_package": "cami-amber",
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"Suite_first_commit_date": "2024-05-20",
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"Suite_owner": "iuc",
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"Suite_parsed_folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber",
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"Suite_runs_(last_5_years)_(usegalaxy.eu)": 195,
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"Suite_runs_(last_5_years)_on_main_servers": 195,
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"Suite_runs_(usegalaxy.eu)": 195,
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"Suite_runs_on_main_servers": 585,
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"Suite_source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/",
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"Suite_users_(last_5_years)_(usegalaxy.eu)": 4,
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"Suite_users_(last_5_years)_on_main_servers": 4,
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"Suite_users_(usegalaxy.eu)": 4,
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"Suite_users_on_main_servers": 12,
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"Suite_version": "2.0.7",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Metagenomics",
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"Tool_IDs": "biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert",
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"bio.tool_ID": "cami-amber",
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"bio.tool_description": "AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation.",
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"bio.tool_name": "AMBER"
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}

‎data/cemitool/cemitool.galaxy.json‎

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"Suite_users_(usegalaxy.eu)": 32,
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"Suite_users_(usegalaxy.org)": 61,
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"Suite_users_on_main_servers": 279,
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"Suite_version": "1.26.0",
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"Suite_version_status": "To update",
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"Suite_version": "1.30.0",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Transcriptomics, RNA, Statistics, Single Cell",
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"Tool_IDs": "cemitool",
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"bio.tool_ID": "cemitool",

‎data/checkm/checkm.galaxy.json‎

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"EDAM_topics": "Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management",
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"Homepage": "https://github.com/chklovski/CheckM2",
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"Latest_suite_conda_package_version": "1.0.2",
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"Number_of_tools_on_UseGalaxy.fr": 1,
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"Number_of_tools_on_UseGalaxy.org_(Main)": 1,
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"Suite_ID": "checkm2",
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"Suite_conda_package": "checkm2",

‎data/cutadapt/cutadapt.galaxy.json‎

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"Suite_users_(usegalaxy.org)": 20162,
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"Suite_users_(usegalaxy.org.au)": 3627,
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"Suite_users_on_main_servers": 104072,
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"Suite_version": "4.9",
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"Suite_version_status": "To update",
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"Suite_version": "5.0",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Fasta Manipulation, Fastq Manipulation, Sequence Analysis",
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"Tool_IDs": "cutadapt",
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"bio.tool_ID": "cutadapt",

‎data/dada2/dada2.galaxy.json‎

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"Suite_users_(usegalaxy.org)": 5317,
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"Suite_users_(usegalaxy.org.au)": 394,
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"Suite_users_on_main_servers": 25281,
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"Suite_version_status": "To update",
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"Suite_version": "1.34.0",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Metagenomics",
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"Tool_IDs": "dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts",
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"bio.tool_ID": "dada2",

‎data/deeparg/deeparg.galaxy.json‎

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{
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"Description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes",
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"EDAM_operations": "Antimicrobial resistance prediction, Antimicrobial resistance prediction",
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"EDAM_reduced_operations": "Antimicrobial resistance prediction, Antimicrobial resistance prediction",
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"EDAM_reduced_topics": "Microbiology",
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"EDAM_topics": "Microbiology",
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"Homepage": "https://github.com/gaarangoa/deeparg",
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"Latest_suite_conda_package_version": "1.0.4",
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"Suite_ID": "deeparg",
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"Suite_conda_package": "deeparg",
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"Suite_first_commit_date": "2024-10-07",
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"Suite_owner": "iuc",
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"Suite_parsed_folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg",
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"Suite_source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/deeparg",
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"Suite_version": "1.0.4",
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"Suite_version_status": "Up-to-date",
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"ToolShed_categories": "Sequence Analysis",
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"Tool_IDs": "deeparg_predict, deeparg_short_reads",
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"bio.tool_ID": "deeparg",
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"bio.tool_description": "A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes.",
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"bio.tool_name": "DeepARG"
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}

‎data/ete/ete.galaxy.json‎

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"EDAM_reduced_topics": "Phylogenetics",
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"EDAM_topics": "Phylogenetics",
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"Homepage": "http://etetoolkit.org",
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"Number_of_tools_on_UseGalaxy.eu": 1,
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"Number_of_tools_on_UseGalaxy.fr": 1,
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"Suite_ID": "ete_treeviewer",
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"Suite_conda_package": "curl",

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