Mercurial > repos > anton > vcfhethom
view vcfhethom.xml @ 3:5731e8c3ffde draft default tip
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author | anton |
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date | Mon, 15 Sep 2014 14:52:32 -0400 |
parents | efba18d7b34b |
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<tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.2"> <requirements> <requirement type="package" version="8a5602bf07">vcflib</requirement> </requirements> <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description> <command> #if str($analysis_type) == "count": vcfhetcount "${vcf_input}" > "${out_file1}" #elif str($analysis_type) == "ratio": vcfhethomratio "${vcf_input}" > "${out_file1}" #elif str($analysis_type) == "allele_count": vcfcountalleles "${vcf_input}" > "${out_file1}" #end if </command> <inputs> <param name="analysis_type" type="select" display="radio" label="Select type of calculation:"> <option value="count">Compute the number of heterozygotes</option> <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option> <option value="allele_count">Compute the total number of alleles</option> </param> <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/> </inputs> <outputs> <data format="tabular" name="out_file1" /> </outputs> <tests> <test> <param name="analysis_type" value="count"/> <param name="vcf_input" value="vcflib.vcf"/> <output name="out_file1" file="vcfhethom-test1.tab"/> </test> <test> <param name="analysis_type" value="ratio"/> <param name="vcf_input" value="vcflib.vcf"/> <output name="out_file1" file="vcfhethom-test2.tab"/> </test> <test> <param name="analysis_type" value="allele_count"/> <param name="vcf_input" value="vcflib.vcf"/> <output name="out_file1" file="vcfhethom-test3.tab"/> </test> </tests> <help> This tool performs three basic calculations: (1) Computes the number of heterozygotes (2) Computes the ratio between heterozygotes and homozygotes (3) Computes the total number of alleles in the input dataset ---- This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). </help> </tool>