Mercurial > repos > melissacline > ucsc_cancer_utilities

diff vcfToMutationVector.xml @ 0:60efb9214eaa

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author melissacline
date Wed, 14 Jan 2015 13:54:03 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfToMutationVector.xml	Wed Jan 14 13:54:03 2015 -0500
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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>