From cbee39b2f8cc29c54710bdba6f8186be61da7ae5 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 16:15:14 +0200 Subject: [PATCH] fix shed.yml lint warning --- .../.shed.yml | 1 + .../.shed.yml | 1 + .../data_manager_pangolin_data/.shed.yml | 1 + .../data_manager_star_index_builder/.shed.yml | 1 + tools/allegro/.shed.yml | 1 + tools/art/.shed.yml | 3 +-- tools/b2btools/.shed.yml | 1 + tools/barrnap/.shed.yml | 4 +++- tools/blastxml_to_gapped_gff3/.shed.yml | 1 + tools/charts/.shed.yml | 1 + tools/collection_column_join/.shed.yml | 1 + tools/collection_element_identifiers/.shed.yml | 1 + tools/column_order_header_sort/.shed.yml | 1 + tools/column_remove_by_header/.shed.yml | 1 + tools/compress_file/.shed.yml | 1 + tools/deg_annotate/.shed.yml | 1 + tools/flair/.shed.yml | 8 ++++++++ tools/genehunter_modscore/.shed.yml | 3 ++- tools/gvcftools/.shed.yml | 4 ++++ tools/hicstuff/.shed.yml | 8 +++++--- tools/hivclustering/.shed.yml | 1 + tools/intermine_galaxy_exchange/.shed.yml | 1 + tools/join_files_by_id/.shed.yml | 1 + tools/king/.shed.yml | 3 ++- tools/merlin/.shed.yml | 3 ++- tools/metagenomeseq/.shed.yml | 1 + tools/multigps/.shed.yml | 3 ++- tools/packaged_annotation_loader/.shed.yml | 1 + tools/pilon/.shed.yml | 2 +- tools/plink/.shed.yml | 3 ++- tools/prinseq/.shed.yml | 1 + tools/progressivemauve/.shed.yml | 1 + tools/quickmerge/.shed.yml | 5 +++++ tools/sbml2sbol/.shed.yml | 1 + tools/snpfreqplot/.shed.yml | 5 +++-- tools/star_fusion/.shed.yml | 1 + tools/strelka/.shed.yml | 15 ++++++++++++++- tools/structure/.shed.yml | 1 + tools/structureharvester/.shed.yml | 3 ++- tools/swift/.shed.yml | 4 ++++ tools/table_compute/.shed.yml | 3 ++- tools/tasmanian_mismatch/.shed.yml | 3 ++- tools/ucsc_blat/.shed.yml | 2 ++ tools/ucsc_tools/fasplit/.shed.yml | 1 + tools/ucsc_tools/twobittofa/.shed.yml | 1 + tools/vcf2maf/.shed.yml | 3 ++- 46 files changed, 94 insertions(+), 19 deletions(-) diff --git a/data_managers/data_manager_gatk_picard_index_builder/.shed.yml b/data_managers/data_manager_gatk_picard_index_builder/.shed.yml index 571e6510f36..6e0bc5ab336 100644 --- a/data_managers/data_manager_gatk_picard_index_builder/.shed.yml +++ b/data_managers/data_manager_gatk_picard_index_builder/.shed.yml @@ -5,4 +5,5 @@ long_description: name: data_manager_gatk_picard_index_builder owner: devteam remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder type: unrestricted diff --git a/data_managers/data_manager_packaged_annotation_data/.shed.yml b/data_managers/data_manager_packaged_annotation_data/.shed.yml index 055755969ff..8ef718d5b9b 100644 --- a/data_managers/data_manager_packaged_annotation_data/.shed.yml +++ b/data_managers/data_manager_packaged_annotation_data/.shed.yml @@ -9,4 +9,5 @@ long_description: | name: data_manager_packaged_annotation_data owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_packaged_annotation_data +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_packaged_annotation_data type: unrestricted diff --git a/data_managers/data_manager_pangolin_data/.shed.yml b/data_managers/data_manager_pangolin_data/.shed.yml index 3a19625e2af..f3224c48dc0 100644 --- a/data_managers/data_manager_pangolin_data/.shed.yml +++ b/data_managers/data_manager_pangolin_data/.shed.yml @@ -7,4 +7,5 @@ long_description: | name: data_manager_pangolin_data owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data type: unrestricted diff --git a/data_managers/data_manager_star_index_builder/.shed.yml b/data_managers/data_manager_star_index_builder/.shed.yml index 85dd50ca3f5..6bfadfcb5a6 100644 --- a/data_managers/data_manager_star_index_builder/.shed.yml +++ b/data_managers/data_manager_star_index_builder/.shed.yml @@ -8,4 +8,5 @@ long_description: | name: data_manager_star_index_builder owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder type: unrestricted diff --git a/tools/allegro/.shed.yml b/tools/allegro/.shed.yml index 0b73d302cea..63592b7a6bb 100644 --- a/tools/allegro/.shed.yml +++ b/tools/allegro/.shed.yml @@ -1,6 +1,7 @@ name: allegro owner: iuc description: Linkage and haplotype analysis from deCODE +long_description: A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity. homepage_url: http://www.decode.com/software/ remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ categories: diff --git a/tools/art/.shed.yml b/tools/art/.shed.yml index d618feb38fd..e231330db9e 100644 --- a/tools/art/.shed.yml +++ b/tools/art/.shed.yml @@ -4,10 +4,9 @@ name: art description: Simulator for Illumina, 454, and SOLiD sequencing data long_description: | Sequencing data simulation tools - - http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ categories: - Sequence Analysis - Data Source remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/art +homepage_url: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ type: unrestricted diff --git a/tools/b2btools/.shed.yml b/tools/b2btools/.shed.yml index d1d316f9eb0..08abf5d02e9 100644 --- a/tools/b2btools/.shed.yml +++ b/tools/b2btools/.shed.yml @@ -5,6 +5,7 @@ long_description: | Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting them to biological events and improving our understanding of the way proteins work. homepage_url: https://bio2byte.be +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools type: unrestricted categories: - Computational chemistry diff --git a/tools/barrnap/.shed.yml b/tools/barrnap/.shed.yml index a650d25372c..0718f0ab6c9 100644 --- a/tools/barrnap/.shed.yml +++ b/tools/barrnap/.shed.yml @@ -4,5 +4,7 @@ description: Contains the Barrnap tool for finding ribosomal RNAs in FASTA seque long_description: | Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. Barrnap now supports Archaea, Eukaryota and Mitochondria. name: barrnap +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap +homepage_url: https://github.com/tseemann/barrnap owner: iuc -type: unrestricted \ No newline at end of file +type: unrestricted diff --git a/tools/blastxml_to_gapped_gff3/.shed.yml b/tools/blastxml_to_gapped_gff3/.shed.yml index 6d6f0eafe48..79499e6042f 100644 --- a/tools/blastxml_to_gapped_gff3/.shed.yml +++ b/tools/blastxml_to_gapped_gff3/.shed.yml @@ -7,4 +7,5 @@ long_description: | name: blastxml_to_gapped_gff3 owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 type: unrestricted diff --git a/tools/charts/.shed.yml b/tools/charts/.shed.yml index f63023e8126..3f2b9202553 100644 --- a/tools/charts/.shed.yml +++ b/tools/charts/.shed.yml @@ -6,6 +6,7 @@ long_description: | The pre-processing is done by this tool. Noteworthy, many chart types like e.g. Bar diagrams and Scatterplots, do not require data pre-processing. owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ type: unrestricted name: charts description: Enables advanced visualization options in Galaxy Charts diff --git a/tools/collection_column_join/.shed.yml b/tools/collection_column_join/.shed.yml index 4d8fb591192..fdb431d11af 100644 --- a/tools/collection_column_join/.shed.yml +++ b/tools/collection_column_join/.shed.yml @@ -6,3 +6,4 @@ long_description: | name: collection_column_join owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join diff --git a/tools/collection_element_identifiers/.shed.yml b/tools/collection_element_identifiers/.shed.yml index 9a58992e906..581b892f627 100644 --- a/tools/collection_element_identifiers/.shed.yml +++ b/tools/collection_element_identifiers/.shed.yml @@ -4,3 +4,4 @@ description: Extract element identifiers of a collection name: collection_element_identifiers owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers diff --git a/tools/column_order_header_sort/.shed.yml b/tools/column_order_header_sort/.shed.yml index d4f06900132..fb0de6ea3e9 100644 --- a/tools/column_order_header_sort/.shed.yml +++ b/tools/column_order_header_sort/.shed.yml @@ -6,3 +6,4 @@ long_description: | name: column_order_header_sort owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort diff --git a/tools/column_remove_by_header/.shed.yml b/tools/column_remove_by_header/.shed.yml index 7c92462dfcd..7081949f35d 100644 --- a/tools/column_remove_by_header/.shed.yml +++ b/tools/column_remove_by_header/.shed.yml @@ -6,3 +6,4 @@ long_description: | name: column_remove_by_header owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header diff --git a/tools/compress_file/.shed.yml b/tools/compress_file/.shed.yml index e95bced2cb1..037d407faea 100644 --- a/tools/compress_file/.shed.yml +++ b/tools/compress_file/.shed.yml @@ -6,4 +6,5 @@ long_description: | name: compress_file owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file type: unrestricted diff --git a/tools/deg_annotate/.shed.yml b/tools/deg_annotate/.shed.yml index f756ff0ab94..f636ffff92f 100644 --- a/tools/deg_annotate/.shed.yml +++ b/tools/deg_annotate/.shed.yml @@ -8,4 +8,5 @@ long_description: | name: deg_annotate owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate type: unrestricted diff --git a/tools/flair/.shed.yml b/tools/flair/.shed.yml index 76231c5fc44..aa4a3865c30 100644 --- a/tools/flair/.shed.yml +++ b/tools/flair/.shed.yml @@ -1,6 +1,10 @@ name: flair owner: iuc description: FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. +long_description: | + FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform + definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been + used for nanopore cDNA, native RNA, and PacBio sequencing reads. homepage_url: https://github.com/BrooksLabUCSC/flair remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair type: unrestricted @@ -12,4 +16,8 @@ auto_tool_repositories: suite: name: "suite_flair" description: FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. + long_description: | + FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform + definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been + used for nanopore cDNA, native RNA, and PacBio sequencing reads. type: repository_suite_definition diff --git a/tools/genehunter_modscore/.shed.yml b/tools/genehunter_modscore/.shed.yml index 9192a62f3b4..48355fd107c 100644 --- a/tools/genehunter_modscore/.shed.yml +++ b/tools/genehunter_modscore/.shed.yml @@ -1,7 +1,8 @@ name: genehunter_modscore owner: iuc description: Maximised LOD score pedigree analysis utility -homepage_url: https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-modscore/index.html +long_description: A MOD-score analysis in which parametric LOD scores are maximized over the parameters of the trait model +homepage_url: https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ categories: - Variant Analysis diff --git a/tools/gvcftools/.shed.yml b/tools/gvcftools/.shed.yml index 53b5719a235..4632aacd163 100644 --- a/tools/gvcftools/.shed.yml +++ b/tools/gvcftools/.shed.yml @@ -4,6 +4,10 @@ owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools homepage_url: https://github.com/sequencing/gvcftools type: unrestricted +long_description: | + gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files. + gVCF are VCF 4.1 files which follow a set of conventions for representing all sites + in the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. auto_tool_repositories: name_template: "{{ tool_id }}" description_template: "Wrapper for ngsutils tool: {{ tool_name }}" diff --git a/tools/hicstuff/.shed.yml b/tools/hicstuff/.shed.yml index 941578e75ac..4c4de4dcc81 100644 --- a/tools/hicstuff/.shed.yml +++ b/tools/hicstuff/.shed.yml @@ -1,6 +1,10 @@ +owner: iuc categories: - Sequence Analysis homepage_url: https://github.com/koszullab/hicstuff +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff +long_description: A toolkit to generate and manipulate Hi-C matrices +type: unrestricted auto_tool_repositories: name_template: "{{ tool_id }}" description_template: "{{ tool_name }} (from the hicstuff tool suite)" @@ -8,6 +12,4 @@ suite: name: suite_hicstuff description: A toolkit to generate and manipulate Hi-C matrices long_description: A toolkit to generate and manipulate Hi-C matrices -owner: iuc -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff -type: unrestricted + diff --git a/tools/hivclustering/.shed.yml b/tools/hivclustering/.shed.yml index bfb73a98d6f..03b80e47a30 100644 --- a/tools/hivclustering/.shed.yml +++ b/tools/hivclustering/.shed.yml @@ -1,6 +1,7 @@ name: hivclustering owner: iuc description: Infers transmission networks from pairwise distances inferred by tn93 +long_description: Infers transmission networks from pairwise distances inferred by tn93 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ homepage_url: https://pypi.org/project/hivclustering/ type: unrestricted diff --git a/tools/intermine_galaxy_exchange/.shed.yml b/tools/intermine_galaxy_exchange/.shed.yml index e80e469125d..aa896e3f670 100644 --- a/tools/intermine_galaxy_exchange/.shed.yml +++ b/tools/intermine_galaxy_exchange/.shed.yml @@ -6,3 +6,4 @@ long_description: | name: intermine_galaxy_exchange owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange +homepage_url: https://github.com/intermine diff --git a/tools/join_files_by_id/.shed.yml b/tools/join_files_by_id/.shed.yml index 9b3c3bc518c..83f8df59ccc 100755 --- a/tools/join_files_by_id/.shed.yml +++ b/tools/join_files_by_id/.shed.yml @@ -9,4 +9,5 @@ long_description: | categories: - Text Manipulation remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id type: unrestricted diff --git a/tools/king/.shed.yml b/tools/king/.shed.yml index dd025bd5ebb..0331f672646 100644 --- a/tools/king/.shed.yml +++ b/tools/king/.shed.yml @@ -1,7 +1,8 @@ name: king owner: iuc description: Kinship-based INference for Gwas +long_description: Kinship-based INference for Gwas (KING) is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study homepage_url: http://people.virginia.edu/~wc9c/KING/ remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ categories: - - Variant Analysis \ No newline at end of file + - Variant Analysis diff --git a/tools/merlin/.shed.yml b/tools/merlin/.shed.yml index 1dc6302b419..9087aa12b7a 100644 --- a/tools/merlin/.shed.yml +++ b/tools/merlin/.shed.yml @@ -1,7 +1,8 @@ name: merlin owner: iuc description: Pedigree Analysis package +long_description: MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around homepage_url: http://csg.sph.umich.edu/abecasis/Merlin/ remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ categories: - - Variant Analysis \ No newline at end of file + - Variant Analysis diff --git a/tools/metagenomeseq/.shed.yml b/tools/metagenomeseq/.shed.yml index 4c5486bee8a..c274b7e1e10 100644 --- a/tools/metagenomeseq/.shed.yml +++ b/tools/metagenomeseq/.shed.yml @@ -6,4 +6,5 @@ long_description: | name: metagenomeseq_normalization owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq +homepage_url: https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html type: unrestricted diff --git a/tools/multigps/.shed.yml b/tools/multigps/.shed.yml index 7326a959431..390ddc05b59 100644 --- a/tools/multigps/.shed.yml +++ b/tools/multigps/.shed.yml @@ -1,13 +1,14 @@ name: multigps owner: iuc description: Analyzes collections of multi-condition ChIP-seq data. -homepage_url: http://mahonylab.org/software/multigps/ long_description: | Contains a tool that runs MultiGPS, a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions. MultiGPS encourages consistency in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS loads all data to memory, so you will need a lot of available memory if you are running analysis over many conditions or large datasets. +homepage_url: http://mahonylab.org/software/multigps/ +remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps" type: unrestricted categories: - ChIP-seq diff --git a/tools/packaged_annotation_loader/.shed.yml b/tools/packaged_annotation_loader/.shed.yml index f3ae6476e2e..71cb6c1998b 100644 --- a/tools/packaged_annotation_loader/.shed.yml +++ b/tools/packaged_annotation_loader/.shed.yml @@ -9,4 +9,5 @@ long_description: | name: packaged_annotation_loader owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader type: unrestricted diff --git a/tools/pilon/.shed.yml b/tools/pilon/.shed.yml index e815a070fb4..9dc59ba9d81 100644 --- a/tools/pilon/.shed.yml +++ b/tools/pilon/.shed.yml @@ -5,8 +5,8 @@ long_description: | Pilon is a software tool which can be used to: * Automatically improve draft assemblies * Find variation among strains, including large event detection - https://github.com/broadinstitute/pilon/wiki name: pilon owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon +homepage_url: https://github.com/broadinstitute/pilon/wiki type: unrestricted diff --git a/tools/plink/.shed.yml b/tools/plink/.shed.yml index b170cd2ba61..5006ec6ea10 100644 --- a/tools/plink/.shed.yml +++ b/tools/plink/.shed.yml @@ -1,6 +1,7 @@ name: plink owner: iuc -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. +description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. +long_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. homepage_url: https://www.cog-genomics.org/plink remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink type: unrestricted diff --git a/tools/prinseq/.shed.yml b/tools/prinseq/.shed.yml index 4a8863d210d..0fd0b3739de 100644 --- a/tools/prinseq/.shed.yml +++ b/tools/prinseq/.shed.yml @@ -2,6 +2,7 @@ categories: - Fastq Manipulation - Metagenomics description: PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets +long_description: PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets homepage_url: http://prinseq.sourceforge.net/manual.html name: prinseq owner: iuc diff --git a/tools/progressivemauve/.shed.yml b/tools/progressivemauve/.shed.yml index eed2486b610..77d7cec38ab 100644 --- a/tools/progressivemauve/.shed.yml +++ b/tools/progressivemauve/.shed.yml @@ -20,4 +20,5 @@ long_description: | name: progressivemauve owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve +homepage_url: http://darlinglab.org/mauve/user-guide/progressivemauve.html type: unrestricted diff --git a/tools/quickmerge/.shed.yml b/tools/quickmerge/.shed.yml index 14ec27427f9..85a8e674502 100644 --- a/tools/quickmerge/.shed.yml +++ b/tools/quickmerge/.shed.yml @@ -6,3 +6,8 @@ categories: - Assembly type: unrestricted description: Merge long-read and hybrid assemblies to increase contiguity +long_description: | + The program 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. diff --git a/tools/sbml2sbol/.shed.yml b/tools/sbml2sbol/.shed.yml index 569e95f9b41..a0bf5524467 100644 --- a/tools/sbml2sbol/.shed.yml +++ b/tools/sbml2sbol/.shed.yml @@ -2,6 +2,7 @@ categories: - Synthetic Biology description: Convert SBML to SBOL format homepage_url: https://github.com/neilswainston/SbmlToSbol +remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol" long_description: 'This tool takes a pathway model (encoded in SBML) as input and returns a collection of placeholders for the subsequent design of the synthetic DNA that is required to encode the enzymes defined in the pathway model (encoded in SBOL).' name: sbml2sbol owner: iuc diff --git a/tools/snpfreqplot/.shed.yml b/tools/snpfreqplot/.shed.yml index fe5472c6ca4..e14c2f49776 100644 --- a/tools/snpfreqplot/.shed.yml +++ b/tools/snpfreqplot/.shed.yml @@ -1,7 +1,8 @@ name: snpfreqplot owner: iuc -description: Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data -homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ +description: A plotting app to visualise the SNPs across a region +long_description: Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data +homepage_url: https://github.com/BrownfieldPlantLab/SNPFreqPlot remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ categories: - Variant Analysis diff --git a/tools/star_fusion/.shed.yml b/tools/star_fusion/.shed.yml index 58a766b0635..90e81938a1c 100644 --- a/tools/star_fusion/.shed.yml +++ b/tools/star_fusion/.shed.yml @@ -12,4 +12,5 @@ long_description: | name: star_fusion owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion +homepage_url: https://github.com/STAR-Fusion/STAR-Fusion type: unrestricted diff --git a/tools/strelka/.shed.yml b/tools/strelka/.shed.yml index 3d13da4b152..211eec415b7 100644 --- a/tools/strelka/.shed.yml +++ b/tools/strelka/.shed.yml @@ -2,6 +2,19 @@ name: strelka owner: iuc remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka" homepage_url: "https://github.com/Illumina/strelka/" +long_description: | + Strelka2 is a fast and accurate small variant caller optimized + for analysis of germline variation in small cohorts and somatic + variation in tumor/normal sample pairs. The germline caller employs an + efficient tiered haplotype model to improve accuracy and provide read-backed + phasing, adaptively selecting between assembly and a faster alignment-based + haplotyping approach at each variant locus. The germline caller also analyzes + input sequencing data using a mixture-model indel error estimation method to + improve robustness to indel noise. The somatic calling model improves on the + original Strelka method for liquid and late-stage tumor analysis by accounting + for possible tumor cell contamination in the normal sample. A final empirical + variant re-scoring step using random forest models trained on various call + quality features has been added to both callers to further improve precision. categories: - "Variant Analysis" auto_tool_repositories: @@ -22,4 +35,4 @@ suite: original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A final empirical variant re-scoring step using random forest models trained on various call - quality features has been added to both callers to further improve precision. \ No newline at end of file + quality features has been added to both callers to further improve precision. diff --git a/tools/structure/.shed.yml b/tools/structure/.shed.yml index f5906945448..0b270e11fa2 100644 --- a/tools/structure/.shed.yml +++ b/tools/structure/.shed.yml @@ -14,4 +14,5 @@ long_description: | name: structure owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure +homepage_url: https://web.stanford.edu/group/pritchardlab/structure.html type: unrestricted diff --git a/tools/structureharvester/.shed.yml b/tools/structureharvester/.shed.yml index 6142e406a32..1c3e87e079e 100644 --- a/tools/structureharvester/.shed.yml +++ b/tools/structureharvester/.shed.yml @@ -3,8 +3,9 @@ categories: - Variant Analysis description: for parsing STRUCTURE outputs and for performing the Evanno method long_description: | - http://taylor0.biology.ucla.edu/structureHarvester/ + structureHarvester.py is a Python script capable of extracting all the relevant data from STRUCTURE results files name: structureharvester owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester +homepage_url: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ type: unrestricted diff --git a/tools/swift/.shed.yml b/tools/swift/.shed.yml index 987f0a04338..2ee3e2a9142 100644 --- a/tools/swift/.shed.yml +++ b/tools/swift/.shed.yml @@ -1,6 +1,10 @@ name: swiftlink owner: iuc description: Parallel MCMC Linkage Analysis +long_description: | + A multipoint parametric linkage analysis tool for large consanguineous pedigrees and is + primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm + based program, i.e. many markers, but larger pedigree homepage_url: https://github.com/ajm/swiftlink remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ categories: diff --git a/tools/table_compute/.shed.yml b/tools/table_compute/.shed.yml index cfe6eb361b0..75395872d9e 100644 --- a/tools/table_compute/.shed.yml +++ b/tools/table_compute/.shed.yml @@ -1,10 +1,11 @@ categories: - Text Manipulation +description: Perform general-purpose table operations long_description: | Operations such as; sorting, subselecting, duplicating, expression evaluation, and more. These can be performed on the row, column, or element level. owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute +homepage_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute type: unrestricted name: table_compute -description: Perform general-purpose table operations diff --git a/tools/tasmanian_mismatch/.shed.yml b/tools/tasmanian_mismatch/.shed.yml index 1a2eab7e12f..e729fcce8ef 100644 --- a/tools/tasmanian_mismatch/.shed.yml +++ b/tools/tasmanian_mismatch/.shed.yml @@ -3,6 +3,7 @@ description: Analysis of positional mismatches long_description: A tool to count and visualize the distribution of positional mismatches from reads of High throughput DNA sequencing experiments owner: iuc type: unrestricted -remote_repository_url: https://github.com/nebiolabs/tasmanian-mismatch +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch +homepage_url: https://github.com/nebiolabs/tasmanian-mismatch categories: - Sequence Analysis diff --git a/tools/ucsc_blat/.shed.yml b/tools/ucsc_blat/.shed.yml index 38eb5e8efc3..d6bcf705401 100644 --- a/tools/ucsc_blat/.shed.yml +++ b/tools/ucsc_blat/.shed.yml @@ -1,7 +1,9 @@ name: ucsc_blat owner: yating-l description: Standalone blat sequence search command line tool +long_description: Standalone blat sequence search command line tool homepage_url: http://genome.ucsc.edu/goldenPath/help/blatSpec.html +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ type: unrestricted categories: - Sequence Analysis diff --git a/tools/ucsc_tools/fasplit/.shed.yml b/tools/ucsc_tools/fasplit/.shed.yml index cafbebd8774..537b99c632c 100644 --- a/tools/ucsc_tools/fasplit/.shed.yml +++ b/tools/ucsc_tools/fasplit/.shed.yml @@ -1,6 +1,7 @@ name: ucsc_fasplit owner: iuc description: faSplit is a tool to split a single FASTA file into several files +long_description: faSplit is a tool to split a single FASTA file into several files homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit type: unrestricted diff --git a/tools/ucsc_tools/twobittofa/.shed.yml b/tools/ucsc_tools/twobittofa/.shed.yml index 903ea76897d..43bd19a4fdb 100644 --- a/tools/ucsc_tools/twobittofa/.shed.yml +++ b/tools/ucsc_tools/twobittofa/.shed.yml @@ -1,6 +1,7 @@ name: ucsc_twobittofa owner: iuc description: twoBitToFa is a tool to convert all or part of .2bit file to FASTA +long_description: twoBitToFa is a tool to convert all or part of .2bit file to FASTA homepage_url: https://genome.ucsc.edu/goldenpath/help/twoBit.html remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa type: unrestricted diff --git a/tools/vcf2maf/.shed.yml b/tools/vcf2maf/.shed.yml index 4ee83751ff0..53962bdb174 100644 --- a/tools/vcf2maf/.shed.yml +++ b/tools/vcf2maf/.shed.yml @@ -10,4 +10,5 @@ long_description: | name: vcf2maf owner: iuc remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf -type: unrestricted \ No newline at end of file +homepage_url: https://github.com/mskcc/vcf2maf +type: unrestricted