Mercurial > repos > melissacline > ucsc_cancer_utilities

comparison vcfToXena.xml @ 48:a38cc72edd75

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xena header
author jingchunzhu
date Fri, 14 Aug 2015 00:04:41 -0700
parents 23d98125d20c
children 986bca7bc318
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47:23d98125d20c 48:a38cc72edd75
2 <description>Convert vcf To Xena ready mutation data</description> 2 <description>Convert vcf To Xena ready mutation data</description>
3 <command> 3 <command>
4 java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config 4 java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config
5 -i vcf -upDownStreamLen 5000 $genome 5 -i vcf -upDownStreamLen 5000 $genome
6 $input > $__tool_directory__/tmp ; 6 $input > $__tool_directory__/tmp ;
7 cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output 7 python $__tool_directory__/xenaHeader.py $snpeff_output;
8 cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output
8 </command> 9 </command>
9 <inputs> 10 <inputs>
10 <param format="vcf" name="input" type="data" label="Input VCF file"/> 11 <param format="vcf" name="input" type="data" label="Input VCF file"/>
11 <param name="genome" type="select" label="Genome"> 12 <param name="genome" type="select" label="Genome">
12 <option value="hg19">hg19</option> 13 <option value="hg19">hg19</option>