Mercurial > repos > melissacline > ucsc_cancer_utilities
view vcfToMutationVector.xml @ 40:72dc9215623d
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author | jingchunzhu |
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date | Fri, 31 Jul 2015 21:29:17 -0700 |
parents | 60efb9214eaa |
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<tool id="vcfToMutationVector" description="Convert SNP output VCF to Xena mutation input format" name="SnpEff VCF To Mutation Vector" version="0.0.1"> <description> Given a VCF generated by snpEff, generate mutation data for input to Xena </description> <command interpreter="python"> vcfToMutationVector.py $inputVcf --trinity $isTrinity > $mutationVector </command> <inputs> <param name="inputVcf" format="tabular" type="data" label="snpEff Output VCF"/> <param name="isTrinity" type="boolean" truevalue="1" falsevalue="0"> <label>Was the input VCF produced from Trinity output?</label> </param> </inputs> <outputs> <data name="mutationVector" format="tabular"/> </outputs> <help> This tool will take a VCF file generated by snpEff and format it appropriately for input to Xena. </help> </tool>