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annotate vcfToXena.xml @ 55:1093078e7976

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merge mutation data conform to new mutationVector data standard
author jingchunzhu
date Fri, 18 Sep 2015 10:24:39 -0700
parents 986bca7bc318
children
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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 $input > $__tool_directory__/tmp_$input.name ;
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6 python $__tool_directory__/xenaHeader.py $snpeff_output;
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7 cat $__tool_directory__/tmp_$input.name | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output;
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8 rm $__tool_directory__/tmp_$input.name
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9 </command>
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10 <inputs>
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11 <param format="vcf" name="input" type="data" label="Input VCF file"/>
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12 <param name="genome" type="select" label="Genome">
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13 <option value="hg19">hg19</option>
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14 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="snpeff_output" label="${input.name}.mutationVector" />
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19 </outputs>
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20 <help>
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21 This tool convert vcf files to xena ready positional mutation data files.
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22 </help>
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23 </tool>
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