view vcfToMutationVector.xml @ 1:ae91153d3fc2

Updated synapseGetDataset.py to automatically unzip if the file downloaded is a zip archive.

<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>