Mercurial > repos > melissacline > ucsc_cancer_utilities

annotate vcfToXena.xml @ 45:e2627dcbd8b9

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start vcfToXena
author jingchunzhu
date Thu, 13 Aug 2015 21:48:02 -0700
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children 23d98125d20c
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1 <tool id="vcfToXena" name="vcfToXena" version="0.1">
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2 <description>Vcf To Xena positional 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 > $snpeff_output
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7 </command>
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8 <inputs>
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9 <param format="vcf" name="input" type="data" label="Input VCF file"/>
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10 <param name="genome" type="select" label="Genome">
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11 <option value="hg19">hg19</option>
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12 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="vcf" name="snpeff_output" />
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17 </outputs>
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18 <help>
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19 This tool convert vcf files to xena ready positional mutation data files.
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20 </help>
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21 </tool>
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