diff --git a/.github/workflows/fetch_all_tools.yaml b/.github/workflows/fetch_all_tools.yaml index ec8f87da..2224d125 100644 --- a/.github/workflows/fetch_all_tools.yaml +++ b/.github/workflows/fetch_all_tools.yaml @@ -61,9 +61,11 @@ jobs: - uses: actions/setup-python@v5 - name: Install requirement run: python -m pip install -r requirements.txt - - name: Run script - run: | - cat results/repositories*.list_tools.tsv > results/all_tools.tsv + - name: Merge all tools + run: | #merge files with only one header -> https://stackoverflow.com/questions/16890582/unixmerge-multiple-csv-files-with-same-header-by-keeping-the-header-of-the-firs + awk 'FNR==1 && NR!=1{next;}{print}' results/repositories*.list_tools.tsv > results/all_tools.tsv + - name: Wordcloud and interactive table + run: | bash ./bin/extract_all_tools_downstream.sh - name: Commit all tools # add or commit any changes in results if there was a change, merge with main and push as bot diff --git a/results/all_tools.tsv b/results/all_tools.tsv index 8dbb3794..0dc1f947 100644 --- a/results/all_tools.tsv +++ b/results/all_tools.tsv @@ -25,7 +25,6 @@ unzip 508 unzip Unzip file To update https://github.com/bmcv Convert Format w4mclassfilter 3 w4mclassfilter Filter W4M data by values or metadata To update https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper Metabolomics w4mclassfilter eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master 0.98.19 r-base (0/1) (1/1) (1/1) w4mcorcov 5 w4mcorcov OPLS-DA Contrasts of Univariate Results To update https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper Metabolomics w4mcorcov eschen42 https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master 0.98.18 r-base (0/1) (1/1) (1/1) w4mjoinpn 2 w4mjoinpn Join positive- and negative-mode W4M datasets To update https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper Metabolomics w4mjoinpn eschen42 https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master 0.98.2 coreutils 8.25 (0/1) (1/1) (1/1) -Galaxy wrapper id https://usegalaxy.eu usage Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu 10x_bamtofastq 46 10x_bamtofastq Converts 10x Genomics BAM to FASTQ Up-to-date https://github.com/10XGenomics/bamtofastq Convert Formats 10x_bamtofastq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1.4.1 10x_bamtofastq 1.4.1 (0/1) (0/1) (1/1) add_line_to_file 193 add_line_to_file Adds a text line to the beginning or end of a file. To update Text Manipulation add_line_to_file bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 0.1.0 coreutils 8.25 (1/1) (1/1) (1/1) agat 42 agat GTF/GFF analysis toolkit agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. Data handling, Genome annotation Genomics Up-to-date https://github.com/NBISweden/AGAT Convert Formats, Statistics, Fasta Manipulation agat bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat 1.2.0 agat 1.2.0 (0/1) (0/1) (1/1) @@ -135,7 +134,6 @@ vcftools_slice 24 vcftools_slice Subset VCF dataset by genomic regions To u vcftools_subset 17 vcftools_subset Select samples from a VCF dataset To update https://vcftools.github.io/ Variant Analysis vcftools_subset devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset 0.1 tabix 1.11 (0/1) (0/1) (1/1) venn_list 248 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) wtdbg 116 wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. wtdbg2 wtdbg2 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. Genome assembly, De-novo assembly Sequence assembly, Sequencing Up-to-date https://github.com/ruanjue/wtdbg2 Assembly wtdbg bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg 2.5 wtdbg 2.5 (0/1) (0/1) (1/1) -Galaxy wrapper id https://usegalaxy.eu usage Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu abricate 1257 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) adapter_removal 37 adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. adapterremoval AdapterRemoval 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. Sequence trimming, Sequence merging, Primer removal Up-to-date https://github.com/MikkelSchubert/adapterremoval Fasta Manipulation, Sequence Analysis adapter_removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ 2.3.3 adapterremoval 2.3.3 (0/1) (0/1) (1/1) aldex2 13 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 ALDEx2 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. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 (0/1) (0/1) (1/1) @@ -452,7 +450,6 @@ winnowmap 27 winnowmap A long-read mapping tool optimized for mapping ONT and Pa xpath 3 xpath XPath XML querying tool To update http://search.cpan.org/dist/XML-XPath/ Text Manipulation xpath iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath perl-xml-xpath 1.47 (0/1) (0/1) (1/1) yahs 64 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) zerone 2 zerone ChIP-seq discretization and quality control Up-to-date https://github.com/nanakiksc/zerone ChIP-seq zerone iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone 1.0 zerone 1.0 (0/1) (0/1) (1/1) -Galaxy wrapper id https://usegalaxy.eu usage Galaxy tool ids Description bio.tool id bio.tool name bio.tool description EDAM operation EDAM topic Status Source ToolShed categories ToolShed id Galaxy wrapper owner Galaxy wrapper source Galaxy wrapper version Conda id Conda version https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.eu bed_to_protein_map 49 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) bigwig_to_bedgraph 200 bigwig_to_bedgraph Converts a bigWig file to bedGraph format To update http://artbio.fr Convert Formats bigwig_to_bedgraph artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 377+galaxy1 ucsc-bigwigtobedgraph 448 (0/1) (0/1) (1/1) blast2go 101 blast2go Maps BLAST results to GO annotation terms To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Ontology Manipulation, Sequence Analysis blast2go peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe (0/1) (0/1) (0/1)