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1 <tool id="vcfToXena" name="vcfToXena" version="0.1">
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2 <description>Convert vcf To Xena ready mutation data</description>
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3 <command>
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4 java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config
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5 -i vcf -upDownStreamLen 5000 $genome
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6 $input > $__tool_directory__/tmp ;
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7 cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output
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8 </command>
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9 <inputs>
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10 <param format="vcf" name="input" type="data" label="Input VCF file"/>
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11 <param name="genome" type="select" label="Genome">
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12 <option value="hg19">hg19</option>
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13 </param>
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14
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="snpeff_output" label="${input.name}.mutationVector" />
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18 </outputs>
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19 <help>
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20 This tool convert vcf files to xena ready positional mutation data files.
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21 </help>
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22 </tool>
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