Mercurial > repos > gandres > vcftools_filter_stats_diversity
view vcftools_main/VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml @ 1:0f67ed444d47 draft
Uploaded
author | gandres |
---|---|
date | Thu, 02 Jul 2015 11:07:45 -0400 |
parents | 3b1436a9a6e5 |
children |
line wrap: on
line source
<tool id="sniplay_vcftoolsslidingwindow" name="VCF tools SlidingWindow" version="1.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Make diversity computation with sliding window </description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="0.1.12b">vcftools</requirement> </requirements> <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> <!-- tool_binary -v --> </version_command> <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> VCFToolsSlidingWindow.pl --input $filein --out $fileout_label --step $step --window $window && mv ${fileout_label}.vcftools.log $filelog && mv ${fileout_label}.Tajima.D ${fileout_taj} && mv ${fileout_label}.TsTv ${fileout_tstv} && mv ${fileout_label}.windowed.pi ${fileout_windowed} && mv ${fileout_label}.snpden ${fileout_snp} </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> <param name="fileout_label" type="text" value="snp_density" optional="false" label="Output file basename"/> <param name="window" type="integer" value="200000" optional="false" label="Window size (in bp)"/> <param name="step" type="integer" value="50000" optional="false" label="Step size (in bp)"/> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_snp" format="tabular" label="${fileout_label}.snpden" /> <data name="fileout_taj" format="tabular" label="${fileout_label}.Tajima.D" /> <data name="fileout_tstv" format="tabular" label="${fileout_label}.TsTv" /> <data name="fileout_windowed" format="tabular" label="${fileout_label}.windowed.pi" /> <data name="filelog" format="txt" label="${fileout_label}.log" /> </outputs> <!-- [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" /> </stdio> <!-- [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="sample.vcf" /> <output name="fileout_annot" file="result.annotation" /> <output name="fileout_het" file="result.het" /> <output name="fileout_imiss" file="result.imiss" /> <output name="fileout_sum" file="result.TsTv.summary" /> <output name="filelog" file="result.log" /> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. 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** Andres Gwendoline, Institut Français de Bioinformatique. .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr --------------------------------------------------- ================ VCF tools filter ================ ----------- Description ----------- | Compute statistics on VCF file | For further informations on VCFtools, please visite the VCFtools website. | .. _VCFtools: http://vcftools.sourceforge.net ----------------- Workflow position ----------------- **Upstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= **Downstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= ---------- Input file ---------- VCF file VCF file with all SNPs ---------- Parameters ---------- 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 --------------------------------------------------- --------------- 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 Parameters ========== 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> </tool>