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author | dereeper |
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date | Sun, 04 Feb 2024 14:19:20 +0000 |
parents | aad8f697f86b |
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<tool id="sniplay_vcftoolsslidingwindow" name="VCFtools SlidingWindow" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description>VCFtools SlidingWindow</description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> <requirement type="package" version="0.1.14">vcftools</requirement> <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement> </requirements> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> <regex match="No such file or directory" level="fatal" description="Failed to install vcftools package" /> </stdio> <!-- [REQUIRED] The command to execute --> <command interpreter="bash"> vcfToolsSlidingWindow.sh ${filein} $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} #if $group : $group ${fileout_fst} ${fileout_fst_marker} ${fileout_taj_combined} ${fileout_windowed_combined} ${fileout_tstv_combined} ${fileout_snp_combined} #else : "none" #end if </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> <param name="fileout_label" type="text" value="snp_density" optional="false" label="Output file basename"/> <param name="window" type="integer" value="200000" optional="false" label="Window size (in bp)"/> <param name="group" type="data" format="tab" optional="True" label="(optionnal) Groups" help="Each line of the file should be : Indiv;Pop" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_snp" format="txt" label="${fileout_label}.snpden" /> <data name="fileout_taj" format="txt" label="${fileout_label}.Tajima.D" /> <data name="fileout_tstv" format="txt" label="${fileout_label}.TsTv" /> <data name="fileout_windowed" format="txt" label="${fileout_label}.windowed.pi" /> <data name="filelog" format="txt" label="${fileout_label}.log" /> <data name="fileout_fst" format="txt" label="${fileout_label}.fst.txt"> <filter>(group != None)</filter> </data> <data name="fileout_fst_marker" format="txt" label="${fileout_label}.fst.by_marker.genes.txt"> <filter>(group != None)</filter> </data> <data name="fileout_windowed_combined" format="txt" label="${fileout_label}.combined.pi.txt" > <filter>(group != None)</filter> </data> <data name="fileout_taj_combined" format="txt" label="${fileout_label}.combined.dtajima.txt" > <filter>(group != None)</filter> </data> <data name="fileout_tstv_combined" format="txt" label="${fileout_label}.combined.TsTv.txt" > <filter>(group != None)</filter> </data> <data name="fileout_snp_combined" format="txt" label="${fileout_label}.combined.snpden.txt" > <filter>(group != None)</filter> </data> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="filein" value="sliding-sample_group.vcf" /> <param name="group" value="sliding-groups.txt" /> <output name="fileout_snp" file="sliding-result2.snpden" /> <output name="fileout_taj" file="sliding-result2.Tajima.D" /> <output name="fileout_tstv" file="sliding-result2.TsTv" /> <output name="fileout_windowed" file="sliding-result2.windowed.pi" /> <output name="fileout_fst" file="sliding-result2.fst.txt" /> <output name="fileout_fst_marker" file="sliding-result2.fst.by_marker.genes.txt" /> <output name="fileout_taj_combined" file="sliding-result2.combined.dtajima.txt" /> <output name="fileout_windowed_combined" file="sliding-result2.combined.pi.txt" /> <output name="fileout_tstv_combined" file="sliding-result2.combined.TsTv.txt" /> <output name="fileout_snp_combined" file="sliding-result2.combined.snpden.txt" /> </test> <test> <param name="filein" value="sample.vcf" /> <output name="fileout_snp" file="sliding-result.snpden" /> <output name="fileout_taj" file="sliding-result.Tajima.D" /> <output name="fileout_tstv" file="sliding-result.TsTv" /> <output name="fileout_windowed" file="sliding-result.windowed.pi" /> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help><![CDATA[ .. class:: infomark **Authors** Adam Auton, Petr Danecek and Anthony Marcketta (C++ Module) : VCFtools (http://vcftools.sourceforge.net) | **Please cite** "The Variant Call Format and VCFtools", Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, **Bioinformatics**, 2011 .. class:: infomark **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- ======================= VCF tools SlidingWindow ======================= ----------- Description ----------- | Make diversity computation with sliding window. | For further informations on VCFtools, please visit the VCFtools website_. .. _website: http://vcftools.sourceforge.net ------------ Dependencies ------------ VCFtools vcftools_ 0.1.14, Conda version VCFtools Perl libraries perl-vcftools-vcf_ 0.1.14, Conda version Bioperl perl-bioperl_ 1.6.924, Conda version .. _vcftools: https://anaconda.org/bioconda/vcftools .. _perl-vcftools-vcf: https://anaconda.org/bioconda/perl-vcftools-vcf .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl ---------- Input file ---------- VCF file VCF file with all SNPs --------- Parameter --------- Output file basename Prefix for the output VCF file ------------ Output files ------------ .snpden file SNP density along chromosomes (number of variants) .Tajima.D file Tajima's D statistics .TsTv file TsTv (Transition/transversion ratio) .windowed.pi file Nucleotide diversity Pi .log file Log and parameters of vcftools execution --------------------------------------------------- --------------- Working example --------------- Input files =========== VCF file --------- :: #fileformat=VCFv4.1 #FILTER=<ID=LowQual,Description="Low quality"> #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> [...] CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 Parameter ========= Output name -> snp_density Output files ============ .snpden file ------------ :: CHROM BIN_START SNP_COUNT VARIANTS/KB chr1 0 4955 24.775 .Tajima.D file -------------- :: CHROM BIN_START N_SNPS TajimaD chr1 0 3737 -nan .TsTv file ---------- :: CHROM BinStart SNP_count Ts/Tv chr1 0 4928 1.88356 .windowed.pi file ----------------- :: CHROM BIN_START BIN_END N_VARIANTS PI chr1 1 200000 3764 0.01882 ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex"> @article{Danecek01082011, author = {Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A. and Banks, Eric and DePristo, Mark A. and Handsaker, Robert E. and Lunter, Gerton and Marth, Gabor T. and Sherry, Stephen T. and McVean, Gilean and Durbin, Richard and 1000 Genomes Project Analysis Group}, title = {The variant call format and VCFtools}, volume = {27}, number = {15}, pages = {2156-2158}, year = {2011}, doi = {10.1093/bioinformatics/btr330}, abstract ={Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.Availability: http://vcftools.sourceforge.netContact: rd@sanger.ac.uk}, URL = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.full.pdf+html}, journal = {Bioinformatics} } </citation> </citations> </tool>