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| { | ||
| "Conda id": "abricate", | ||
| "Conda version": "1.0.1", | ||
| "Description": "Mass screening of contigs for antiobiotic resistance genes", | ||
| "EDAM operation": "Antimicrobial resistance prediction", | ||
| "EDAM topic": "Genomics, Microbiology", | ||
| "Galaxy tool ids": "abricate, abricate_list, abricate_summary", | ||
| "Galaxy wrapper id": "abricate", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/", | ||
| "Galaxy wrapper version": "1.0.1", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 1764, | ||
| "Source": "https://github.com/tseemann/abricate", | ||
| "Status": "Up-to-date", | ||
| "ToolShed categories": "Sequence Analysis", | ||
| "ToolShed id": "abricate", | ||
| "Total tool usage (usegalaxy.eu)": 496717, | ||
| "bio.tool description": "Mass screening of contigs for antimicrobial resistance or virulence genes.", | ||
| "bio.tool id": "ABRicate", | ||
| "bio.tool ids": "ABRicate", | ||
| "bio.tool name": "ABRicate", | ||
| "https://usegalaxy.eu": "(3/3)", | ||
| "https://usegalaxy.fr": "(3/3)", | ||
| "https://usegalaxy.org": "(3/3)", | ||
| "https://usegalaxy.org.au": "(3/3)" | ||
| } |
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| { | ||
| "Conda id": "abritamr", | ||
| "Conda version": "1.0.17", | ||
| "Description": "A pipeline for running AMRfinderPlus and collating results into functional classes", | ||
| "EDAM operation": "Antimicrobial resistance prediction", | ||
| "EDAM topic": "Microbiology, Public health and epidemiology, Infectious disease", | ||
| "Galaxy tool ids": "abritamr", | ||
| "Galaxy wrapper id": "abritamr", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr", | ||
| "Galaxy wrapper version": "1.0.14", | ||
| "Source": "https://zenodo.org/record/7370628", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Sequence Analysis", | ||
| "ToolShed id": "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.", | ||
| "bio.tool id": "abritamr", | ||
| "bio.tool ids": "abritamr", | ||
| "bio.tool name": "abriTAMR", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "abyss", | ||
| "Conda version": "2.3.7", | ||
| "Description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", | ||
| "EDAM operation": "Genome assembly, De-novo assembly, Scaffolding", | ||
| "EDAM topic": "Sequence assembly", | ||
| "Galaxy tool ids": "abyss-pe", | ||
| "Galaxy wrapper id": "abyss", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss", | ||
| "Galaxy wrapper version": "2.3.7", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 391, | ||
| "Source": "http://www.bcgsc.ca/platform/bioinfo/software/abyss", | ||
| "Status": "Up-to-date", | ||
| "ToolShed categories": "Assembly", | ||
| "ToolShed id": "abyss", | ||
| "Total tool usage (usegalaxy.eu)": 4278, | ||
| "bio.tool description": "De novo genome sequence assembler using short reads.", | ||
| "bio.tool id": "abyss", | ||
| "bio.tool ids": "abyss", | ||
| "bio.tool name": "ABySS", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(1/1)" | ||
| } |
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| { | ||
| "Conda id": "adapterremoval", | ||
| "Conda version": "2.3.3", | ||
| "Description": "Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.", | ||
| "EDAM operation": "Sequence trimming, Sequence merging, Primer removal", | ||
| "Galaxy tool ids": "adapter_removal", | ||
| "Galaxy wrapper id": "adapter_removal", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/", | ||
| "Galaxy wrapper version": "2.3.3", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 37, | ||
| "Source": "https://github.com/MikkelSchubert/adapterremoval", | ||
| "Status": "Up-to-date", | ||
| "ToolShed categories": "Fasta Manipulation, Sequence Analysis", | ||
| "ToolShed id": "adapter_removal", | ||
| "Total tool usage (usegalaxy.eu)": 217, | ||
| "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.", | ||
| "bio.tool id": "adapterremoval", | ||
| "bio.tool ids": "adapterremoval", | ||
| "bio.tool name": "AdapterRemoval", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "agat", | ||
| "Conda version": "1.4.0", | ||
| "Description": "GTF/GFF analysis toolkit", | ||
| "EDAM operation": "Data handling, Genome annotation", | ||
| "EDAM topic": "Genomics", | ||
| "Galaxy tool ids": "agat", | ||
| "Galaxy wrapper id": "agat", | ||
| "Galaxy wrapper owner": "bgruening", | ||
| "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", | ||
| "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/agat", | ||
| "Galaxy wrapper version": "1.2.0", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 42, | ||
| "Source": "https://github.com/NBISweden/AGAT", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Convert Formats, Statistics, Fasta Manipulation", | ||
| "ToolShed id": "agat", | ||
| "Total tool usage (usegalaxy.eu)": 481, | ||
| "bio.tool description": "Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.", | ||
| "bio.tool id": "agat", | ||
| "bio.tool ids": "agat", | ||
| "bio.tool name": "AGAT", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(1/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "bioconductor-aldex2", | ||
| "Conda version": "1.34.0", | ||
| "Description": "Performs analysis Of differential abundance taking sample variation into account", | ||
| "EDAM operation": "Statistical inference", | ||
| "EDAM topic": "Gene expression, Statistics and probability", | ||
| "Galaxy tool ids": "aldex2", | ||
| "Galaxy wrapper id": "aldex2", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2", | ||
| "Galaxy wrapper version": "1.26.0", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 13, | ||
| "Source": "https://github.com/ggloor/ALDEx_bioc", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Metagenomics", | ||
| "ToolShed id": "aldex2", | ||
| "Total tool usage (usegalaxy.eu)": 129, | ||
| "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.", | ||
| "bio.tool id": "aldex2", | ||
| "bio.tool ids": "aldex2", | ||
| "bio.tool name": "ALDEx2", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "allegro", | ||
| "Conda version": "3", | ||
| "Description": "Linkage and haplotype analysis from deCODE", | ||
| "EDAM operation": "Sequence motif discovery", | ||
| "EDAM topic": "Sequence analysis, Transcription factors and regulatory sites, DNA", | ||
| "Galaxy tool ids": "allegro", | ||
| "Galaxy wrapper id": "allegro", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/", | ||
| "Galaxy wrapper version": "@VER@.0", | ||
| "Source": "http://www.decode.com/software/", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Variant Analysis", | ||
| "ToolShed id": "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.", | ||
| "bio.tool id": "allegro", | ||
| "bio.tool ids": "allegro", | ||
| "bio.tool name": "Allegro", | ||
| "https://usegalaxy.eu": "(0/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "bioconductor-amplican", | ||
| "Conda version": "1.24.0", | ||
| "Description": "AmpliCan is an analysis tool for genome editing.", | ||
| "EDAM operation": "Alignment, Standardisation and normalisation", | ||
| "EDAM topic": "PCR experiment, Statistics and probability", | ||
| "Galaxy tool ids": "amplican", | ||
| "Galaxy wrapper id": "amplican", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican", | ||
| "Galaxy wrapper version": "1.14.0", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 12, | ||
| "Source": "https://github.com/valenlab/amplican", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Sequence Analysis", | ||
| "ToolShed id": "amplican", | ||
| "Total tool usage (usegalaxy.eu)": 53, | ||
| "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.", | ||
| "bio.tool id": "amplican", | ||
| "bio.tool ids": "amplican", | ||
| "bio.tool name": "amplican", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Description": "ampvis2", | ||
| "EDAM operation": "Analysis, Visualisation", | ||
| "EDAM topic": "Biodiversity", | ||
| "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", | ||
| "Galaxy wrapper id": "ampvis2", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2", | ||
| "Galaxy wrapper version": "2.8.6", | ||
| "Source": "https://github.com/MadsAlbertsen/ampvis2/", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Metagenomics", | ||
| "ToolShed id": "ampvis2", | ||
| "bio.tool description": "ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.", | ||
| "bio.tool id": "ampvis", | ||
| "bio.tool ids": "ampvis", | ||
| "bio.tool name": "ampvis", | ||
| "https://usegalaxy.eu": "(19/19)", | ||
| "https://usegalaxy.fr": "(0/19)", | ||
| "https://usegalaxy.org": "(0/19)", | ||
| "https://usegalaxy.org.au": "(0/19)" | ||
| } |
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| { | ||
| "Conda id": "ncbi-amrfinderplus", | ||
| "Conda version": "3.12.8", | ||
| "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", | ||
| "Galaxy tool ids": "amrfinderplus", | ||
| "Galaxy wrapper id": "amrfinderplus", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus", | ||
| "Galaxy wrapper version": "3.11.26", | ||
| "Source": "https://github.com/ncbi/amr", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Sequence Analysis", | ||
| "ToolShed id": "AMRFinderPlus", | ||
| "Total tool usage (usegalaxy.eu)": 591, | ||
| "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", | ||
| "bio.tool id": "amrfinderplus", | ||
| "bio.tool ids": "amrfinderplus", | ||
| "bio.tool name": "AMRFinderPlus", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(1/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "bioconductor-ancombc", | ||
| "Conda version": "2.4.0", | ||
| "Description": "Performs analysis of compositions of microbiomes with bias correction.", | ||
| "EDAM operation": "DNA barcoding", | ||
| "EDAM topic": "Microbial ecology, Metagenomics, Taxonomy", | ||
| "Galaxy tool ids": "ancombc", | ||
| "Galaxy wrapper id": "ancombc", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc", | ||
| "Galaxy wrapper version": "1.4.0", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 4, | ||
| "Source": "https://github.com/FrederickHuangLin/ANCOMBC", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Metagenomics", | ||
| "ToolShed id": "ancombc", | ||
| "Total tool usage (usegalaxy.eu)": 7, | ||
| "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.", | ||
| "bio.tool id": "ancombc", | ||
| "bio.tool ids": "ancombc", | ||
| "bio.tool name": "ANCOMBC", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(0/1)", | ||
| "https://usegalaxy.org.au": "(0/1)" | ||
| } |
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| { | ||
| "Conda id": "bioconductor-org.hs.eg.db", | ||
| "Conda version": "3.18.0", | ||
| "Description": "annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages", | ||
| "EDAM operation": "Annotation", | ||
| "Galaxy tool ids": "annotatemyids", | ||
| "Galaxy wrapper id": "annotatemyids", | ||
| "Galaxy wrapper owner": "iuc", | ||
| "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", | ||
| "Galaxy wrapper version": "3.18.0", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 1175, | ||
| "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids", | ||
| "Status": "Up-to-date", | ||
| "ToolShed categories": "Genome annotation", | ||
| "ToolShed id": "annotatemyids", | ||
| "Total tool usage (usegalaxy.eu)": 26115, | ||
| "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.", | ||
| "bio.tool id": "annotatemyids", | ||
| "bio.tool ids": "annotatemyids", | ||
| "bio.tool name": "annotatemyids", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(1/1)", | ||
| "https://usegalaxy.org": "(1/1)", | ||
| "https://usegalaxy.org.au": "(1/1)" | ||
| } |
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| { | ||
| "Conda id": "antismash", | ||
| "Conda version": "7.1.0", | ||
| "Description": "Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters", | ||
| "EDAM operation": "Sequence clustering, Gene prediction, Differential gene expression analysis", | ||
| "EDAM topic": "Molecular interactions, pathways and networks, Gene and protein families", | ||
| "Galaxy tool ids": "antismash", | ||
| "Galaxy wrapper id": "antismash", | ||
| "Galaxy wrapper owner": "bgruening", | ||
| "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/antismash", | ||
| "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash", | ||
| "Galaxy wrapper version": "6.1.1", | ||
| "No. of tool users (2022-2023) (usegalaxy.eu)": 279, | ||
| "Source": "https://antismash.secondarymetabolites.org", | ||
| "Status": "To update", | ||
| "ToolShed categories": "Sequence Analysis", | ||
| "ToolShed id": "antismash", | ||
| "Total tool usage (usegalaxy.eu)": 14596, | ||
| "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.", | ||
| "bio.tool id": "antismash", | ||
| "bio.tool ids": "antismash", | ||
| "bio.tool name": "antiSMASH", | ||
| "https://usegalaxy.eu": "(1/1)", | ||
| "https://usegalaxy.fr": "(0/1)", | ||
| "https://usegalaxy.org": "(1/1)", | ||
| "https://usegalaxy.org.au": "(1/1)" | ||
| } |
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