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view vcfToMutationVector.xml @ 37:e81019e3ac99

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Updated synapseGetDataset to look at the filename rather than the (no longer existant) content type field to determine if the data is in zip format
author melissacline
date Mon, 27 Jul 2015 16:29:24 -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>