From 2a3f586c0fe9448ca5cc4b2da8eb94ce55bf8863 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 27 Jan 2020 16:44:26 +0100 Subject: [PATCH 1/2] this add new bioconda yaml files, for tools that are currently missing from bio.tools --- data/bam2fasta/bioconda_bam2fasta.yaml | 8 ++++++++ .../bioconda_bold-identification.yaml | 8 ++++++++ data/chorus2/bioconda_chorus2.yaml | 8 ++++++++ .../bioconda_extract_fasta_seq.yaml | 7 +++++++ data/faqcs/bioconda_faqcs.yaml | 6 ++++++ data/gem_mapper/bioconda_gem_mapper.yaml | 6 ++++++ data/ispcr/bioconda_ispcr.yaml | 6 ++++++ data/ivar/bioconda_ivar.yaml | 8 ++++++++ data/krakenhll/bioconda_krakenhll.yaml | 6 ++++++ data/ksw/bioconda_ksw.yaml | 6 ++++++ data/magicblast/bioconda_magicblast.yaml | 17 +++++++++++++++++ data/malt/bioconda_malt.yaml | 5 +++++ data/malva/bioconda_malva.yaml | 5 +++++ data/manta9235/bioconda_manta9235.yaml | 5 +++++ data/mgkit/bioconda_mgkit.yaml | 6 ++++++ data/miniax/bioconda_miniax.yaml | 7 +++++++ data/mirtop/bioconda_mirtop.yaml | 6 ++++++ data/mutmap/bioconda_mutmap.yaml | 6 ++++++ data/ngmerge/bioconda_ngmerge.yaml | 6 ++++++ data/pgcgap/bioconda_pgcgap.yaml | 8 ++++++++ data/phame/bioconda_phame.yaml | 6 ++++++ data/phylocsf/bioconda_phylocsf.yaml | 7 +++++++ data/pirate/bioconda_pirate.yaml | 7 +++++++ data/piret/bioconda_piret.yaml | 5 +++++ data/popera/bioconda_popera.yaml | 7 +++++++ data/qtlseq/bioconda_qtlseq.yaml | 6 ++++++ .../bioconda_referenceseeker.yaml | 8 ++++++++ data/sepp-refgg138/bioconda_sepp-refgg138.yaml | 7 +++++++ .../bioconda_sepp-refsilva128.yaml | 7 +++++++ data/sepp/bioconda_sepp.yaml | 7 +++++++ data/shark/bioconda_shark.yaml | 6 ++++++ data/slimm/bioconda_slimm.yaml | 5 +++++ .../super_distance/bioconda_super_distance.yaml | 6 ++++++ .../taxonomy_ranks/bioconda_taxonomy_ranks.yaml | 8 ++++++++ data/thesias/bioconda_thesias.yaml | 5 +++++ data/wham6216/bioconda_wham6216.yaml | 6 ++++++ data/womtool/bioconda_womtool.yaml | 7 +++++++ data/xhmm/bioconda_xhmm.yaml | 5 +++++ 38 files changed, 255 insertions(+) create mode 100644 data/bam2fasta/bioconda_bam2fasta.yaml create mode 100644 data/bold-identification/bioconda_bold-identification.yaml create mode 100644 data/chorus2/bioconda_chorus2.yaml create mode 100644 data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml create mode 100644 data/faqcs/bioconda_faqcs.yaml create mode 100644 data/gem_mapper/bioconda_gem_mapper.yaml create mode 100644 data/ispcr/bioconda_ispcr.yaml create mode 100644 data/ivar/bioconda_ivar.yaml create mode 100644 data/krakenhll/bioconda_krakenhll.yaml create mode 100644 data/ksw/bioconda_ksw.yaml create mode 100644 data/magicblast/bioconda_magicblast.yaml create mode 100644 data/malt/bioconda_malt.yaml create mode 100644 data/malva/bioconda_malva.yaml create mode 100644 data/manta9235/bioconda_manta9235.yaml create mode 100644 data/mgkit/bioconda_mgkit.yaml create mode 100644 data/miniax/bioconda_miniax.yaml create mode 100644 data/mirtop/bioconda_mirtop.yaml create mode 100644 data/mutmap/bioconda_mutmap.yaml create mode 100644 data/ngmerge/bioconda_ngmerge.yaml create mode 100644 data/pgcgap/bioconda_pgcgap.yaml create mode 100644 data/phame/bioconda_phame.yaml create mode 100644 data/phylocsf/bioconda_phylocsf.yaml create mode 100644 data/pirate/bioconda_pirate.yaml create mode 100644 data/piret/bioconda_piret.yaml create mode 100644 data/popera/bioconda_popera.yaml create mode 100644 data/qtlseq/bioconda_qtlseq.yaml create mode 100644 data/referenceseeker/bioconda_referenceseeker.yaml create mode 100644 data/sepp-refgg138/bioconda_sepp-refgg138.yaml create mode 100644 data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml create mode 100644 data/sepp/bioconda_sepp.yaml create mode 100644 data/shark/bioconda_shark.yaml create mode 100644 data/slimm/bioconda_slimm.yaml create mode 100644 data/super_distance/bioconda_super_distance.yaml create mode 100644 data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml create mode 100644 data/thesias/bioconda_thesias.yaml create mode 100644 data/wham6216/bioconda_wham6216.yaml create mode 100644 data/womtool/bioconda_womtool.yaml create mode 100644 data/xhmm/bioconda_xhmm.yaml diff --git a/data/bam2fasta/bioconda_bam2fasta.yaml b/data/bam2fasta/bioconda_bam2fasta.yaml new file mode 100644 index 0000000000000..10f87a7911a3d --- /dev/null +++ b/data/bam2fasta/bioconda_bam2fasta.yaml @@ -0,0 +1,8 @@ +dev_url: https://github.com/czbiohub/bam2fasta +home: https://github.com/czbiohub/bam2fasta +license: MIT License +license_family: MIT +license_file: LICENSE +name: bam2fasta +summary: 'bam2fasta: cli tool to convert bam to fastas' +version: 1.0.1 diff --git a/data/bold-identification/bioconda_bold-identification.yaml b/data/bold-identification/bioconda_bold-identification.yaml new file mode 100644 index 0000000000000..1ffdd32530d14 --- /dev/null +++ b/data/bold-identification/bioconda_bold-identification.yaml @@ -0,0 +1,8 @@ +home: https://github.com/linzhi2013/bold_identification +license: GNU General Public v3 or later (GPLv3+) +license_family: GPL3 +license_file: LICENSE +name: bold-identification +summary: A tool for taxonomic assignment for given sequences using the BOLD database + (http://www.boldsystems.org/index.php) +version: 0.0.25 diff --git a/data/chorus2/bioconda_chorus2.yaml b/data/chorus2/bioconda_chorus2.yaml new file mode 100644 index 0000000000000..7848661dc15a2 --- /dev/null +++ b/data/chorus2/bioconda_chorus2.yaml @@ -0,0 +1,8 @@ +dev_url: https://github.com/zhangtaolab/Chorus2 +doc_url: https://chorus2.readthedocs.io/en/dev/ +home: https://github.com/zhangtaolab/Chorus2 +license: MIT license +name: chorus2 +summary: A pipeline to select oligonucleotides for fluorescence in situ hbridization + (Oligo-FISH). +version: 2.0 diff --git a/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml b/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml new file mode 100644 index 0000000000000..51681075087e8 --- /dev/null +++ b/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml @@ -0,0 +1,7 @@ +home: https://github.com/linzhi2013/extract_fasta_seq +license: GNU General Public v3 or later (GPLv3+) +license_family: GPL3 +license_file: LICENSE +name: extract_fasta_seq +summary: To extract specific fasta sequences from a fasta file. +version: 0.0.1 diff --git a/data/faqcs/bioconda_faqcs.yaml b/data/faqcs/bioconda_faqcs.yaml new file mode 100644 index 0000000000000..9a88bed98e103 --- /dev/null +++ b/data/faqcs/bioconda_faqcs.yaml @@ -0,0 +1,6 @@ +home: https://github.com/LANL-Bioinformatics/FaQCs +license: BSD 3-Clause +license_file: LICENSE +name: faqcs +summary: Quality Control of Next Generation Sequencing Data. +version: 2.09 diff --git a/data/gem_mapper/bioconda_gem_mapper.yaml b/data/gem_mapper/bioconda_gem_mapper.yaml new file mode 100644 index 0000000000000..edda23dc71a86 --- /dev/null +++ b/data/gem_mapper/bioconda_gem_mapper.yaml @@ -0,0 +1,6 @@ +home: https://github.com/smarco/gem3-mapper +license: GPL-3.0 +license_file: LICENSE +name: gem3-mapper +summary: The GEM read mapper (v3). +version: 3.6.1 diff --git a/data/ispcr/bioconda_ispcr.yaml b/data/ispcr/bioconda_ispcr.yaml new file mode 100644 index 0000000000000..108a3b659b522 --- /dev/null +++ b/data/ispcr/bioconda_ispcr.yaml @@ -0,0 +1,6 @@ +home: https://users.soe.ucsc.edu/~kent/ +license: License is hereby granted for personal, academic, and non-profit use. +license_file: README +name: ispcr +summary: In silico PCR +version: 33 diff --git a/data/ivar/bioconda_ivar.yaml b/data/ivar/bioconda_ivar.yaml new file mode 100644 index 0000000000000..bfbdecedbae96 --- /dev/null +++ b/data/ivar/bioconda_ivar.yaml @@ -0,0 +1,8 @@ +dev_url: https://github.com/andersen-lab/ivar +home: https://andersen-lab.github.io/ivar/html/ +license: GPL-3.0 +license_file: LICENSE +name: ivar +summary: iVar is a computational package that contains functions broadly useful for + viral amplicon-based sequencing. +version: 1.0.1 diff --git a/data/krakenhll/bioconda_krakenhll.yaml b/data/krakenhll/bioconda_krakenhll.yaml new file mode 100644 index 0000000000000..ad2f44d28c9c6 --- /dev/null +++ b/data/krakenhll/bioconda_krakenhll.yaml @@ -0,0 +1,6 @@ +home: https://github.com/fbreitwieser/krakenuniq +license: GPLv3 +license_file: LICENSE +name: krakenuniq +summary: Metagenomics classifier with unique k-mer counting for more specific results +version: 0.5.8 diff --git a/data/ksw/bioconda_ksw.yaml b/data/ksw/bioconda_ksw.yaml new file mode 100644 index 0000000000000..e0be33651bc25 --- /dev/null +++ b/data/ksw/bioconda_ksw.yaml @@ -0,0 +1,6 @@ +home: https://github.com/nh13/ksw +license: MIT +license_file: LICENSE +name: ksw +summary: 'Ksw: (interactive) smith-waterman in C' +version: 0.2.1 diff --git a/data/magicblast/bioconda_magicblast.yaml b/data/magicblast/bioconda_magicblast.yaml new file mode 100644 index 0000000000000..1929a6059f8a2 --- /dev/null +++ b/data/magicblast/bioconda_magicblast.yaml @@ -0,0 +1,17 @@ +description: "Magic-BLAST is a tool for mapping large next-generation RNA or DNA \n\ + sequencing runs against a whole genome or transcriptome. Each alignment\noptimizes\ + \ a composite score, taking into account simultaneously the two\nreads of a pair,\ + \ and in case of RNA-seq, locating the candidate introns\nand adding up the score\ + \ of all exons. This is very different from other\nversions of BLAST, where each\ + \ exon is scored as a separate hit and\nread-pairing is ignored.\n\nMagic-BLAST\ + \ incorporates within the NCBI BLAST code framework ideas \ndeveloped in the NCBI\ + \ Magic pipeline, in particular hit extensions by local \nwalk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056),\ + \ and \nrecursive clipping of mismatches near the edges of the reads, which avoids\n\ + accumulating artefactual mismatches near splice sites and is needed to\ndistinguish\ + \ short indels from substitutions near the edges.\n\nMore details about the algorithm\ + \ and comparison with other similar tools\nare presented here:\nhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2996-x.\n" +home: https://ncbi.github.io/magicblast/ +license: Public Domain +name: magicblast +summary: NCBI BLAST next generation read mapper +version: 1.5.0 diff --git a/data/malt/bioconda_malt.yaml b/data/malt/bioconda_malt.yaml new file mode 100644 index 0000000000000..ac7a281b75295 --- /dev/null +++ b/data/malt/bioconda_malt.yaml @@ -0,0 +1,5 @@ +home: http://ab.inf.uni-tuebingen.de/software/malt/ +license: GPLv3 +name: malt +summary: A tool for mapping metagenomic data +version: 0.41 diff --git a/data/malva/bioconda_malva.yaml b/data/malva/bioconda_malva.yaml new file mode 100644 index 0000000000000..bdeea24647e01 --- /dev/null +++ b/data/malva/bioconda_malva.yaml @@ -0,0 +1,5 @@ +home: https://algolab.github.io/malva/ +license: GPL-3.0-or-later +name: malva +summary: genotyping by Mapping-free ALternate-allele detection of known VAriants +version: 1.1.1 diff --git a/data/manta9235/bioconda_manta9235.yaml b/data/manta9235/bioconda_manta9235.yaml new file mode 100644 index 0000000000000..ef0b44a84fba0 --- /dev/null +++ b/data/manta9235/bioconda_manta9235.yaml @@ -0,0 +1,5 @@ +home: https://github.com/Illumina/manta +license: GPLv3 +name: manta +summary: Structural variant and indel caller for mapped sequencing data +version: 1.6.0 diff --git a/data/mgkit/bioconda_mgkit.yaml b/data/mgkit/bioconda_mgkit.yaml new file mode 100644 index 0000000000000..d81588180d332 --- /dev/null +++ b/data/mgkit/bioconda_mgkit.yaml @@ -0,0 +1,6 @@ +home: https://github.com/frubino/mgkit +license: GNU General Public License v2 or later (GPLv2+) +license_family: GPL2 +name: mgkit +summary: Metagenomics Framework +version: 0.4.1 diff --git a/data/miniax/bioconda_miniax.yaml b/data/miniax/bioconda_miniax.yaml new file mode 100644 index 0000000000000..e4bc547c44090 --- /dev/null +++ b/data/miniax/bioconda_miniax.yaml @@ -0,0 +1,7 @@ +home: https://github.com/GATB/minia +license: file +license_file: LICENSE +name: minia +summary: Minia is a short-read assembler based on a de Bruijn graph, capable of assembling + a human genome on a desktop computer in a day. +version: 3.2.1 diff --git a/data/mirtop/bioconda_mirtop.yaml b/data/mirtop/bioconda_mirtop.yaml new file mode 100644 index 0000000000000..ae7d2512aadcc --- /dev/null +++ b/data/mirtop/bioconda_mirtop.yaml @@ -0,0 +1,6 @@ +home: http://github.com/mirtop/mirtop +license: MIT License +license_family: MIT +name: mirtop +summary: Small RNA-seq annotation +version: 0.4.23 diff --git a/data/mutmap/bioconda_mutmap.yaml b/data/mutmap/bioconda_mutmap.yaml new file mode 100644 index 0000000000000..2294f838875b2 --- /dev/null +++ b/data/mutmap/bioconda_mutmap.yaml @@ -0,0 +1,6 @@ +home: https://github.com/YuSugihara/MutMap +license: GPL-3.0-or-later +license_family: GPL +name: mutmap +summary: 'MutMap: pipeline to identify causative mutations responsible for a phenotype' +version: 2.1.3 diff --git a/data/ngmerge/bioconda_ngmerge.yaml b/data/ngmerge/bioconda_ngmerge.yaml new file mode 100644 index 0000000000000..b7bcb76fbad84 --- /dev/null +++ b/data/ngmerge/bioconda_ngmerge.yaml @@ -0,0 +1,6 @@ +home: https://github.com/harvardinformatics/NGmerge +license: MIT +license_file: LICENSE +name: ngmerge +summary: Merging paired-end reads and removing sequencing adapters. +version: 0.3 diff --git a/data/pgcgap/bioconda_pgcgap.yaml b/data/pgcgap/bioconda_pgcgap.yaml new file mode 100644 index 0000000000000..e0adcf0ad0e51 --- /dev/null +++ b/data/pgcgap/bioconda_pgcgap.yaml @@ -0,0 +1,8 @@ +dev_url: https://github.com/liaochenlanruo/pgcgap/tree/master +home: https://github.com/liaochenlanruo/pgcgap/blob/master/README.md +license: GPLv3 +license_family: GPL +license_file: LICENSE +name: pgcgap +summary: A prokaryotic genomics and comparative genomics analysis pipeline +version: 1.0.9 diff --git a/data/phame/bioconda_phame.yaml b/data/phame/bioconda_phame.yaml new file mode 100644 index 0000000000000..e05718ea8b964 --- /dev/null +++ b/data/phame/bioconda_phame.yaml @@ -0,0 +1,6 @@ +home: https://github.com/LANL-Bioinformatics/PhaME +license: GPLV2 +name: phame +summary: A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, + and full genomes. +version: 1.0.3 diff --git a/data/phylocsf/bioconda_phylocsf.yaml b/data/phylocsf/bioconda_phylocsf.yaml new file mode 100644 index 0000000000000..0fa1f85127e92 --- /dev/null +++ b/data/phylocsf/bioconda_phylocsf.yaml @@ -0,0 +1,7 @@ +home: https://github.com/mlin/PhyloCSF/wiki +license: AGPL-3.0 +license_file: LICENSE +name: phylocsf +summary: Phylogenetic analysis of multi-species genome sequence alignments to identify + conserved protein-coding regions +version: 1.0.1 diff --git a/data/pirate/bioconda_pirate.yaml b/data/pirate/bioconda_pirate.yaml new file mode 100644 index 0000000000000..797d6994f4100 --- /dev/null +++ b/data/pirate/bioconda_pirate.yaml @@ -0,0 +1,7 @@ +home: https://github.com/SionBayliss/PIRATE +license: GPL3 +license_family: GPL +license_file: LICENSE +name: pirate +summary: Pangenome analysis and threshold evaluation toolbox +version: 1.0.3 diff --git a/data/piret/bioconda_piret.yaml b/data/piret/bioconda_piret.yaml new file mode 100644 index 0000000000000..550cf4034b7b4 --- /dev/null +++ b/data/piret/bioconda_piret.yaml @@ -0,0 +1,5 @@ +home: https://github.com/mshakya/PyPiReT +license: GPLV2 +name: piret +summary: A tool for conducting RNA seq analysis. +version: 0.3.4 diff --git a/data/popera/bioconda_popera.yaml b/data/popera/bioconda_popera.yaml new file mode 100644 index 0000000000000..193f44b884399 --- /dev/null +++ b/data/popera/bioconda_popera.yaml @@ -0,0 +1,7 @@ +dev_url: https://github.com/forrestzhang/Popera +home: https://github.com/forrestzhang/Popera +license: MIT +license_file: LICENSE +name: popera +summary: A software for DNase I hypersensitive sites identification. +version: 1.0.3 diff --git a/data/qtlseq/bioconda_qtlseq.yaml b/data/qtlseq/bioconda_qtlseq.yaml new file mode 100644 index 0000000000000..3e2f06986f0d5 --- /dev/null +++ b/data/qtlseq/bioconda_qtlseq.yaml @@ -0,0 +1,6 @@ +home: https://github.com/YuSugihara/QTL-seq +license: GPL-3.0-or-later +license_family: GPL +name: qtlseq +summary: 'QTL-seq: pipeline to identify causative mutations responsible for a phenotype' +version: 2.0.7 diff --git a/data/referenceseeker/bioconda_referenceseeker.yaml b/data/referenceseeker/bioconda_referenceseeker.yaml new file mode 100644 index 0000000000000..3c56e8faf9d87 --- /dev/null +++ b/data/referenceseeker/bioconda_referenceseeker.yaml @@ -0,0 +1,8 @@ +dev_url: https://github.com/oschwengers/referenceseeker +home: https://github.com/oschwengers/referenceseeker +license: GPLv3 +license_family: GPL +license_file: LICENSE +name: referenceseeker +summary: Rapid determination of appropriate reference genomes. +version: '1.4' diff --git a/data/sepp-refgg138/bioconda_sepp-refgg138.yaml b/data/sepp-refgg138/bioconda_sepp-refgg138.yaml new file mode 100644 index 0000000000000..d6e08acce86c7 --- /dev/null +++ b/data/sepp-refgg138/bioconda_sepp-refgg138.yaml @@ -0,0 +1,7 @@ +home: https://github.com/smirarab/sepp-refs +license: GPLv3 +license_family: GPL3 +license_file: LICENSE +name: sepp-refgg138 +summary: SATe-enabled phylogenetic placement +version: 4.3.6 diff --git a/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml b/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml new file mode 100644 index 0000000000000..79001f1bc19bd --- /dev/null +++ b/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml @@ -0,0 +1,7 @@ +home: https://github.com/smirarab/sepp-refs +license: GPLv3 +license_family: GPL3 +license_file: LICENSE +name: sepp-refsilva128 +summary: SATe-enabled phylogenetic placement +version: 4.3.6 diff --git a/data/sepp/bioconda_sepp.yaml b/data/sepp/bioconda_sepp.yaml new file mode 100644 index 0000000000000..38d8aeaa653f8 --- /dev/null +++ b/data/sepp/bioconda_sepp.yaml @@ -0,0 +1,7 @@ +home: https://github.com/smirarab/sepp +license: GPLv3 +license_family: GPL3 +license_file: LICENSE +name: sepp +summary: SATe-enabled phylogenetic placement +version: 4.3.10 diff --git a/data/shark/bioconda_shark.yaml b/data/shark/bioconda_shark.yaml new file mode 100644 index 0000000000000..ca3c8938fead2 --- /dev/null +++ b/data/shark/bioconda_shark.yaml @@ -0,0 +1,6 @@ +home: https://algolab.github.io/shark/ +license: GPL-3.0-or-later +license_file: LICENSE +name: shark +summary: Mapping-free filtering of useless RNA-Seq reads +version: 1.0.0 diff --git a/data/slimm/bioconda_slimm.yaml b/data/slimm/bioconda_slimm.yaml new file mode 100644 index 0000000000000..c97f9e69e2985 --- /dev/null +++ b/data/slimm/bioconda_slimm.yaml @@ -0,0 +1,5 @@ +home: https://github.com/seqan/slimm/blob/master/README.md +license: https://github.com/seqan/slimm/blob/master/LICENSE +name: slimm +summary: SLIMM - Species Level Identification of Microbes from Metagenomes +version: 0.3.4 diff --git a/data/super_distance/bioconda_super_distance.yaml b/data/super_distance/bioconda_super_distance.yaml new file mode 100644 index 0000000000000..ec5bce4bb22a7 --- /dev/null +++ b/data/super_distance/bioconda_super_distance.yaml @@ -0,0 +1,6 @@ +home: https://github.com/quadram-institute-bioscience/super_distance +license: GPLv3 +license_file: LICENSE +name: super_distance +summary: Supertree method with distances +version: 1.1.0 diff --git a/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml b/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml new file mode 100644 index 0000000000000..ce111db12f169 --- /dev/null +++ b/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml @@ -0,0 +1,8 @@ +home: https://github.com/linzhi2013/taxonomy_ranks +license: GNU General Public v3 or later (GPLv3+) +license_family: GPL3 +license_file: LICENSE +name: taxonomy_ranks +summary: To get taxonomy ranks information for taxid, species name, or higher ranks + (e.g., genus, family) with ETE3 from NCBI Taxonomy database. +version: 0.0.7 diff --git a/data/thesias/bioconda_thesias.yaml b/data/thesias/bioconda_thesias.yaml new file mode 100644 index 0000000000000..744a5e823a404 --- /dev/null +++ b/data/thesias/bioconda_thesias.yaml @@ -0,0 +1,5 @@ +home: https://github.com/daissi/thesias +license: GPL-3+ +name: thesias +summary: Testing Haplotype Effects In Association Studies +version: 3.1.1 diff --git a/data/wham6216/bioconda_wham6216.yaml b/data/wham6216/bioconda_wham6216.yaml new file mode 100644 index 0000000000000..cf59bf8277c31 --- /dev/null +++ b/data/wham6216/bioconda_wham6216.yaml @@ -0,0 +1,6 @@ +home: https://github.com/zeeev/wham +license: MIT +license_family: MIT +name: wham +summary: Structural variant detection and association testing +version: 1.8.0.1.2017.05.03 diff --git a/data/womtool/bioconda_womtool.yaml b/data/womtool/bioconda_womtool.yaml new file mode 100644 index 0000000000000..032c8e48bfd46 --- /dev/null +++ b/data/womtool/bioconda_womtool.yaml @@ -0,0 +1,7 @@ +home: https://cromwell.readthedocs.io/en/develop/WOMtool/ +license: BSD-3-Clause +license_family: BSD +license_file: LICENSE.txt +name: womtool +summary: Command line utilities for interacting with WDL +version: 48 diff --git a/data/xhmm/bioconda_xhmm.yaml b/data/xhmm/bioconda_xhmm.yaml new file mode 100644 index 0000000000000..03f5fc3e20c1e --- /dev/null +++ b/data/xhmm/bioconda_xhmm.yaml @@ -0,0 +1,5 @@ +home: http://atgu.mgh.harvard.edu/xhmm/index.shtml +license: GPL3 +name: xhmm +summary: XHMM (eXome-Hidden Markov Model). +version: 0.0.0.2016_01_04.cc14e52 From 270aadc66690c931e1d1639f9cd39e40fb70c80e Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 27 Jan 2020 17:14:39 +0100 Subject: [PATCH 2/2] add identifiers and biotools_id --- data/bam2fasta/bioconda_bam2fasta.yaml | 3 +++ data/bold-identification/bioconda_bold-identification.yaml | 3 +++ data/chorus2/bioconda_chorus2.yaml | 3 +++ data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml | 3 +++ data/faqcs/bioconda_faqcs.yaml | 3 +++ data/gem_mapper/bioconda_gem_mapper.yaml | 4 ++++ data/ispcr/bioconda_ispcr.yaml | 3 +++ data/ivar/bioconda_ivar.yaml | 3 +++ data/krakenhll/bioconda_krakenhll.yaml | 3 +++ data/ksw/bioconda_ksw.yaml | 3 +++ data/magicblast/bioconda_magicblast.yaml | 4 ++++ data/malt/bioconda_malt.yaml | 3 +++ data/malva/bioconda_malva.yaml | 3 +++ data/manta9235/bioconda_manta9235.yaml | 3 +++ data/mgkit/bioconda_mgkit.yaml | 4 ++++ data/miniax/bioconda_miniax.yaml | 3 +++ data/mirtop/bioconda_mirtop.yaml | 3 +++ data/mutmap/bioconda_mutmap.yaml | 4 ++++ data/ngmerge/bioconda_ngmerge.yaml | 3 +++ data/pgcgap/bioconda_pgcgap.yaml | 3 +++ data/phame/bioconda_phame.yaml | 3 +++ data/phylocsf/bioconda_phylocsf.yaml | 3 +++ data/pirate/bioconda_pirate.yaml | 4 ++++ data/piret/bioconda_piret.yaml | 3 +++ data/popera/bioconda_popera.yaml | 3 +++ data/qtlseq/bioconda_qtlseq.yaml | 4 ++++ data/referenceseeker/bioconda_referenceseeker.yaml | 3 +++ data/sepp-refgg138/bioconda_sepp-refgg138.yaml | 3 +++ data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml | 3 +++ data/sepp/bioconda_sepp.yaml | 3 +++ data/shark/bioconda_shark.yaml | 3 +++ data/slimm/bioconda_slimm.yaml | 4 ++++ data/super_distance/bioconda_super_distance.yaml | 3 +++ data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml | 3 +++ data/thesias/bioconda_thesias.yaml | 4 ++++ data/wham6216/bioconda_wham6216.yaml | 3 +++ data/womtool/bioconda_womtool.yaml | 3 +++ data/xhmm/bioconda_xhmm.yaml | 5 +++++ 38 files changed, 124 insertions(+) diff --git a/data/bam2fasta/bioconda_bam2fasta.yaml b/data/bam2fasta/bioconda_bam2fasta.yaml index 10f87a7911a3d..4e34f00d73619 100644 --- a/data/bam2fasta/bioconda_bam2fasta.yaml +++ b/data/bam2fasta/bioconda_bam2fasta.yaml @@ -1,5 +1,8 @@ +biotools_id: bam2fasta dev_url: https://github.com/czbiohub/bam2fasta home: https://github.com/czbiohub/bam2fasta +identifiers: +- biotools:bam2fasta license: MIT License license_family: MIT license_file: LICENSE diff --git a/data/bold-identification/bioconda_bold-identification.yaml b/data/bold-identification/bioconda_bold-identification.yaml index 1ffdd32530d14..5d093f6dee505 100644 --- a/data/bold-identification/bioconda_bold-identification.yaml +++ b/data/bold-identification/bioconda_bold-identification.yaml @@ -1,4 +1,7 @@ +biotools_id: bold-identification home: https://github.com/linzhi2013/bold_identification +identifiers: +- biotools:bold-identification license: GNU General Public v3 or later (GPLv3+) license_family: GPL3 license_file: LICENSE diff --git a/data/chorus2/bioconda_chorus2.yaml b/data/chorus2/bioconda_chorus2.yaml index 7848661dc15a2..f0d841a92426f 100644 --- a/data/chorus2/bioconda_chorus2.yaml +++ b/data/chorus2/bioconda_chorus2.yaml @@ -1,6 +1,9 @@ +biotools_id: chorus2 dev_url: https://github.com/zhangtaolab/Chorus2 doc_url: https://chorus2.readthedocs.io/en/dev/ home: https://github.com/zhangtaolab/Chorus2 +identifiers: +- biotools:chorus2 license: MIT license name: chorus2 summary: A pipeline to select oligonucleotides for fluorescence in situ hbridization diff --git a/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml b/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml index 51681075087e8..187a3336e784f 100644 --- a/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml +++ b/data/extract_fasta_seq/bioconda_extract_fasta_seq.yaml @@ -1,4 +1,7 @@ +biotools_id: extract_fasta_seq home: https://github.com/linzhi2013/extract_fasta_seq +identifiers: +- biotools:extract_fasta_seq license: GNU General Public v3 or later (GPLv3+) license_family: GPL3 license_file: LICENSE diff --git a/data/faqcs/bioconda_faqcs.yaml b/data/faqcs/bioconda_faqcs.yaml index 9a88bed98e103..1fbce4dcbf11a 100644 --- a/data/faqcs/bioconda_faqcs.yaml +++ b/data/faqcs/bioconda_faqcs.yaml @@ -1,4 +1,7 @@ +biotools_id: faqcs home: https://github.com/LANL-Bioinformatics/FaQCs +identifiers: +- biotools:faqcs license: BSD 3-Clause license_file: LICENSE name: faqcs diff --git a/data/gem_mapper/bioconda_gem_mapper.yaml b/data/gem_mapper/bioconda_gem_mapper.yaml index edda23dc71a86..e4e08f6eababd 100644 --- a/data/gem_mapper/bioconda_gem_mapper.yaml +++ b/data/gem_mapper/bioconda_gem_mapper.yaml @@ -1,4 +1,8 @@ +biotools_id: gem_mapper home: https://github.com/smarco/gem3-mapper +identifiers: +- doi:10.1038/nmeth.2221 +- biotools:GEM_Mapper license: GPL-3.0 license_file: LICENSE name: gem3-mapper diff --git a/data/ispcr/bioconda_ispcr.yaml b/data/ispcr/bioconda_ispcr.yaml index 108a3b659b522..d6acb9f692071 100644 --- a/data/ispcr/bioconda_ispcr.yaml +++ b/data/ispcr/bioconda_ispcr.yaml @@ -1,4 +1,7 @@ +biotools_id: ispcr home: https://users.soe.ucsc.edu/~kent/ +identifiers: +- biotools:ispcr license: License is hereby granted for personal, academic, and non-profit use. license_file: README name: ispcr diff --git a/data/ivar/bioconda_ivar.yaml b/data/ivar/bioconda_ivar.yaml index bfbdecedbae96..ba51d2afb4f5a 100644 --- a/data/ivar/bioconda_ivar.yaml +++ b/data/ivar/bioconda_ivar.yaml @@ -1,5 +1,8 @@ +biotools_id: ivar dev_url: https://github.com/andersen-lab/ivar home: https://andersen-lab.github.io/ivar/html/ +identifiers: +- biotools:ivar license: GPL-3.0 license_file: LICENSE name: ivar diff --git a/data/krakenhll/bioconda_krakenhll.yaml b/data/krakenhll/bioconda_krakenhll.yaml index ad2f44d28c9c6..833dc5cdcf708 100644 --- a/data/krakenhll/bioconda_krakenhll.yaml +++ b/data/krakenhll/bioconda_krakenhll.yaml @@ -1,4 +1,7 @@ +biotools_id: krakenhll home: https://github.com/fbreitwieser/krakenuniq +identifiers: +- biotools:krakenhll license: GPLv3 license_file: LICENSE name: krakenuniq diff --git a/data/ksw/bioconda_ksw.yaml b/data/ksw/bioconda_ksw.yaml index e0be33651bc25..842e781241084 100644 --- a/data/ksw/bioconda_ksw.yaml +++ b/data/ksw/bioconda_ksw.yaml @@ -1,4 +1,7 @@ +biotools_id: ksw home: https://github.com/nh13/ksw +identifiers: +- biotools:ksw license: MIT license_file: LICENSE name: ksw diff --git a/data/magicblast/bioconda_magicblast.yaml b/data/magicblast/bioconda_magicblast.yaml index 1929a6059f8a2..3fb66d2717895 100644 --- a/data/magicblast/bioconda_magicblast.yaml +++ b/data/magicblast/bioconda_magicblast.yaml @@ -1,3 +1,4 @@ +biotools_id: magicblast description: "Magic-BLAST is a tool for mapping large next-generation RNA or DNA \n\ sequencing runs against a whole genome or transcriptome. Each alignment\noptimizes\ \ a composite score, taking into account simultaneously the two\nreads of a pair,\ @@ -11,6 +12,9 @@ description: "Magic-BLAST is a tool for mapping large next-generation RNA or DNA \ short indels from substitutions near the edges.\n\nMore details about the algorithm\ \ and comparison with other similar tools\nare presented here:\nhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2996-x.\n" home: https://ncbi.github.io/magicblast/ +identifiers: +- biotools:magicblast +- doi:10.1186/s12859-019-2996-x license: Public Domain name: magicblast summary: NCBI BLAST next generation read mapper diff --git a/data/malt/bioconda_malt.yaml b/data/malt/bioconda_malt.yaml index ac7a281b75295..134d30ecf0aaf 100644 --- a/data/malt/bioconda_malt.yaml +++ b/data/malt/bioconda_malt.yaml @@ -1,4 +1,7 @@ +biotools_id: malt home: http://ab.inf.uni-tuebingen.de/software/malt/ +identifiers: +- biotools:malt license: GPLv3 name: malt summary: A tool for mapping metagenomic data diff --git a/data/malva/bioconda_malva.yaml b/data/malva/bioconda_malva.yaml index bdeea24647e01..2ccea13b69a43 100644 --- a/data/malva/bioconda_malva.yaml +++ b/data/malva/bioconda_malva.yaml @@ -1,4 +1,7 @@ +biotools_id: malva home: https://algolab.github.io/malva/ +identifiers: +- biotools:malva license: GPL-3.0-or-later name: malva summary: genotyping by Mapping-free ALternate-allele detection of known VAriants diff --git a/data/manta9235/bioconda_manta9235.yaml b/data/manta9235/bioconda_manta9235.yaml index ef0b44a84fba0..5600584dca71c 100644 --- a/data/manta9235/bioconda_manta9235.yaml +++ b/data/manta9235/bioconda_manta9235.yaml @@ -1,4 +1,7 @@ +biotools_id: manta9235 home: https://github.com/Illumina/manta +identifiers: +- biotools:Manta9235 license: GPLv3 name: manta summary: Structural variant and indel caller for mapped sequencing data diff --git a/data/mgkit/bioconda_mgkit.yaml b/data/mgkit/bioconda_mgkit.yaml index d81588180d332..774becfddc18c 100644 --- a/data/mgkit/bioconda_mgkit.yaml +++ b/data/mgkit/bioconda_mgkit.yaml @@ -1,4 +1,8 @@ +biotools_id: mgkit home: https://github.com/frubino/mgkit +identifiers: +- biotools:mgkit +- doi:10.6084/m9.figshare.1588384 license: GNU General Public License v2 or later (GPLv2+) license_family: GPL2 name: mgkit diff --git a/data/miniax/bioconda_miniax.yaml b/data/miniax/bioconda_miniax.yaml index e4bc547c44090..59ae5dd2949db 100644 --- a/data/miniax/bioconda_miniax.yaml +++ b/data/miniax/bioconda_miniax.yaml @@ -1,4 +1,7 @@ +biotools_id: miniax home: https://github.com/GATB/minia +identifiers: +- biotools:miniax license: file license_file: LICENSE name: minia diff --git a/data/mirtop/bioconda_mirtop.yaml b/data/mirtop/bioconda_mirtop.yaml index ae7d2512aadcc..b32fc53930c5f 100644 --- a/data/mirtop/bioconda_mirtop.yaml +++ b/data/mirtop/bioconda_mirtop.yaml @@ -1,4 +1,7 @@ +biotools_id: mirtop home: http://github.com/mirtop/mirtop +identifiers: +- biotools:mirtop license: MIT License license_family: MIT name: mirtop diff --git a/data/mutmap/bioconda_mutmap.yaml b/data/mutmap/bioconda_mutmap.yaml index 2294f838875b2..35d111672f637 100644 --- a/data/mutmap/bioconda_mutmap.yaml +++ b/data/mutmap/bioconda_mutmap.yaml @@ -1,4 +1,8 @@ +biotools_id: mutmap home: https://github.com/YuSugihara/MutMap +identifiers: +- biotools:mutmap +- doi:10.1038/nbt.2095 license: GPL-3.0-or-later license_family: GPL name: mutmap diff --git a/data/ngmerge/bioconda_ngmerge.yaml b/data/ngmerge/bioconda_ngmerge.yaml index b7bcb76fbad84..fc2ba6e2f82da 100644 --- a/data/ngmerge/bioconda_ngmerge.yaml +++ b/data/ngmerge/bioconda_ngmerge.yaml @@ -1,4 +1,7 @@ +biotools_id: ngmerge home: https://github.com/harvardinformatics/NGmerge +identifiers: +- biotools:ngmerge license: MIT license_file: LICENSE name: ngmerge diff --git a/data/pgcgap/bioconda_pgcgap.yaml b/data/pgcgap/bioconda_pgcgap.yaml index e0adcf0ad0e51..182c38c39d4f6 100644 --- a/data/pgcgap/bioconda_pgcgap.yaml +++ b/data/pgcgap/bioconda_pgcgap.yaml @@ -1,5 +1,8 @@ +biotools_id: pgcgap dev_url: https://github.com/liaochenlanruo/pgcgap/tree/master home: https://github.com/liaochenlanruo/pgcgap/blob/master/README.md +identifiers: +- biotools:pgcgap license: GPLv3 license_family: GPL license_file: LICENSE diff --git a/data/phame/bioconda_phame.yaml b/data/phame/bioconda_phame.yaml index e05718ea8b964..5e5045839375f 100644 --- a/data/phame/bioconda_phame.yaml +++ b/data/phame/bioconda_phame.yaml @@ -1,4 +1,7 @@ +biotools_id: phame home: https://github.com/LANL-Bioinformatics/PhaME +identifiers: +- biotools:phame license: GPLV2 name: phame summary: A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, diff --git a/data/phylocsf/bioconda_phylocsf.yaml b/data/phylocsf/bioconda_phylocsf.yaml index 0fa1f85127e92..4e3efc88d4e1e 100644 --- a/data/phylocsf/bioconda_phylocsf.yaml +++ b/data/phylocsf/bioconda_phylocsf.yaml @@ -1,4 +1,7 @@ +biotools_id: phylocsf home: https://github.com/mlin/PhyloCSF/wiki +identifiers: +- biotools:phyloCSF license: AGPL-3.0 license_file: LICENSE name: phylocsf diff --git a/data/pirate/bioconda_pirate.yaml b/data/pirate/bioconda_pirate.yaml index 797d6994f4100..9944e4f3e9f06 100644 --- a/data/pirate/bioconda_pirate.yaml +++ b/data/pirate/bioconda_pirate.yaml @@ -1,4 +1,8 @@ +biotools_id: pirate home: https://github.com/SionBayliss/PIRATE +identifiers: +- biotools:pirate +- doi:10.1101/598391 license: GPL3 license_family: GPL license_file: LICENSE diff --git a/data/piret/bioconda_piret.yaml b/data/piret/bioconda_piret.yaml index 550cf4034b7b4..4a34e9a14d767 100644 --- a/data/piret/bioconda_piret.yaml +++ b/data/piret/bioconda_piret.yaml @@ -1,4 +1,7 @@ +biotools_id: piret home: https://github.com/mshakya/PyPiReT +identifiers: +- biotools:piret license: GPLV2 name: piret summary: A tool for conducting RNA seq analysis. diff --git a/data/popera/bioconda_popera.yaml b/data/popera/bioconda_popera.yaml index 193f44b884399..7be078b1abe13 100644 --- a/data/popera/bioconda_popera.yaml +++ b/data/popera/bioconda_popera.yaml @@ -1,5 +1,8 @@ +biotools_id: popera dev_url: https://github.com/forrestzhang/Popera home: https://github.com/forrestzhang/Popera +identifiers: +- biotools:popera license: MIT license_file: LICENSE name: popera diff --git a/data/qtlseq/bioconda_qtlseq.yaml b/data/qtlseq/bioconda_qtlseq.yaml index 3e2f06986f0d5..7d98f73a31fc0 100644 --- a/data/qtlseq/bioconda_qtlseq.yaml +++ b/data/qtlseq/bioconda_qtlseq.yaml @@ -1,4 +1,8 @@ +biotools_id: qtlseq home: https://github.com/YuSugihara/QTL-seq +identifiers: +- biotools:qtlseq +- doi:10.1111/tpj.12105 license: GPL-3.0-or-later license_family: GPL name: qtlseq diff --git a/data/referenceseeker/bioconda_referenceseeker.yaml b/data/referenceseeker/bioconda_referenceseeker.yaml index 3c56e8faf9d87..6ad8309e67593 100644 --- a/data/referenceseeker/bioconda_referenceseeker.yaml +++ b/data/referenceseeker/bioconda_referenceseeker.yaml @@ -1,5 +1,8 @@ +biotools_id: referenceseeker dev_url: https://github.com/oschwengers/referenceseeker home: https://github.com/oschwengers/referenceseeker +identifiers: +- biotools:referenceseeker license: GPLv3 license_family: GPL license_file: LICENSE diff --git a/data/sepp-refgg138/bioconda_sepp-refgg138.yaml b/data/sepp-refgg138/bioconda_sepp-refgg138.yaml index d6e08acce86c7..6c723474d1d0b 100644 --- a/data/sepp-refgg138/bioconda_sepp-refgg138.yaml +++ b/data/sepp-refgg138/bioconda_sepp-refgg138.yaml @@ -1,4 +1,7 @@ +biotools_id: sepp-refgg138 home: https://github.com/smirarab/sepp-refs +identifiers: +- biotools:sepp-refgg138 license: GPLv3 license_family: GPL3 license_file: LICENSE diff --git a/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml b/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml index 79001f1bc19bd..6152a5ba7d1cb 100644 --- a/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml +++ b/data/sepp-refsilva128/bioconda_sepp-refsilva128.yaml @@ -1,4 +1,7 @@ +biotools_id: sepp-refsilva128 home: https://github.com/smirarab/sepp-refs +identifiers: +- biotools:sepp-refsilva128 license: GPLv3 license_family: GPL3 license_file: LICENSE diff --git a/data/sepp/bioconda_sepp.yaml b/data/sepp/bioconda_sepp.yaml index 38d8aeaa653f8..105ae1d6deb47 100644 --- a/data/sepp/bioconda_sepp.yaml +++ b/data/sepp/bioconda_sepp.yaml @@ -1,4 +1,7 @@ +biotools_id: sepp home: https://github.com/smirarab/sepp +identifiers: +- biotools:sepp license: GPLv3 license_family: GPL3 license_file: LICENSE diff --git a/data/shark/bioconda_shark.yaml b/data/shark/bioconda_shark.yaml index ca3c8938fead2..ae61743f2ed9d 100644 --- a/data/shark/bioconda_shark.yaml +++ b/data/shark/bioconda_shark.yaml @@ -1,4 +1,7 @@ +biotools_id: shark home: https://algolab.github.io/shark/ +identifiers: +- biotools:shark license: GPL-3.0-or-later license_file: LICENSE name: shark diff --git a/data/slimm/bioconda_slimm.yaml b/data/slimm/bioconda_slimm.yaml index c97f9e69e2985..7ee99491a6d61 100644 --- a/data/slimm/bioconda_slimm.yaml +++ b/data/slimm/bioconda_slimm.yaml @@ -1,4 +1,8 @@ +biotools_id: slimm home: https://github.com/seqan/slimm/blob/master/README.md +identifiers: +- biotools:slimm +- doi:10.7717/peerj.3138 license: https://github.com/seqan/slimm/blob/master/LICENSE name: slimm summary: SLIMM - Species Level Identification of Microbes from Metagenomes diff --git a/data/super_distance/bioconda_super_distance.yaml b/data/super_distance/bioconda_super_distance.yaml index ec5bce4bb22a7..755238063c86e 100644 --- a/data/super_distance/bioconda_super_distance.yaml +++ b/data/super_distance/bioconda_super_distance.yaml @@ -1,4 +1,7 @@ +biotools_id: super_distance home: https://github.com/quadram-institute-bioscience/super_distance +identifiers: +- biotools:super_distance license: GPLv3 license_file: LICENSE name: super_distance diff --git a/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml b/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml index ce111db12f169..de30d94f0ae9c 100644 --- a/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml +++ b/data/taxonomy_ranks/bioconda_taxonomy_ranks.yaml @@ -1,4 +1,7 @@ +biotools_id: taxonomy_ranks home: https://github.com/linzhi2013/taxonomy_ranks +identifiers: +- biotools:taxonomy_ranks license: GNU General Public v3 or later (GPLv3+) license_family: GPL3 license_file: LICENSE diff --git a/data/thesias/bioconda_thesias.yaml b/data/thesias/bioconda_thesias.yaml index 744a5e823a404..3b6f4d873880b 100644 --- a/data/thesias/bioconda_thesias.yaml +++ b/data/thesias/bioconda_thesias.yaml @@ -1,4 +1,8 @@ +biotools_id: thesias home: https://github.com/daissi/thesias +identifiers: +- biotools:THESIAS +- doi:10.1093/bioinformatics/btm058 license: GPL-3+ name: thesias summary: Testing Haplotype Effects In Association Studies diff --git a/data/wham6216/bioconda_wham6216.yaml b/data/wham6216/bioconda_wham6216.yaml index cf59bf8277c31..eca18d0d802fd 100644 --- a/data/wham6216/bioconda_wham6216.yaml +++ b/data/wham6216/bioconda_wham6216.yaml @@ -1,4 +1,7 @@ +biotools_id: wham6216 home: https://github.com/zeeev/wham +identifiers: +- biotools:Wham6216 license: MIT license_family: MIT name: wham diff --git a/data/womtool/bioconda_womtool.yaml b/data/womtool/bioconda_womtool.yaml index 032c8e48bfd46..2c501e8f91b2b 100644 --- a/data/womtool/bioconda_womtool.yaml +++ b/data/womtool/bioconda_womtool.yaml @@ -1,4 +1,7 @@ +biotools_id: womtool home: https://cromwell.readthedocs.io/en/develop/WOMtool/ +identifiers: +- biotools:womtool license: BSD-3-Clause license_family: BSD license_file: LICENSE.txt diff --git a/data/xhmm/bioconda_xhmm.yaml b/data/xhmm/bioconda_xhmm.yaml index 03f5fc3e20c1e..e581c7e476fdc 100644 --- a/data/xhmm/bioconda_xhmm.yaml +++ b/data/xhmm/bioconda_xhmm.yaml @@ -1,4 +1,9 @@ +biotools_id: xhmm home: http://atgu.mgh.harvard.edu/xhmm/index.shtml +identifiers: +- biotools:xhmm +- doi:10.1016/j.ajhg.2012.08.005 +- doi:10.1002/0471142905.hg0723s81 license: GPL3 name: xhmm summary: XHMM (eXome-Hidden Markov Model).