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1 <tool id="vcfToMutationVector" description="Convert SNP output VCF to Xena mutation input format" name="SnpEff VCF To Mutation Vector" version="0.0.1">
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2 <description>
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3 Given a VCF generated by snpEff, generate mutation data for input to Xena
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4 </description>
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5 <command interpreter="python">
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6 vcfToMutationVector.py $inputVcf --trinity $isTrinity > $mutationVector
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7 </command>
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8 <inputs>
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9 <param name="inputVcf" format="tabular" type="data" label="snpEff Output VCF"/>
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10 <param name="isTrinity" type="boolean" truevalue="1" falsevalue="0">
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11 <label>Was the input VCF produced from Trinity output?</label>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data name="mutationVector" format="tabular"/>
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16 </outputs>
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17 <help>
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18 This tool will take a VCF file generated by snpEff and format it appropriately for input
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19 to Xena.
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20 </help>
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21 </tool>
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