Mercurial > repos > melissacline > ucsc_cancer_utilities
changeset 49:986bca7bc318
multiple files
| author | jingchunzhu |
|---|---|
| date | Fri, 14 Aug 2015 00:17:55 -0700 |
| parents | a38cc72edd75 |
| children | b6f5d2d1b047 |
| files | vcfToXena.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/vcfToXena.xml Fri Aug 14 00:04:41 2015 -0700 +++ b/vcfToXena.xml Fri Aug 14 00:17:55 2015 -0700 @@ -2,10 +2,10 @@ <description>Convert vcf To Xena ready mutation data</description> <command> java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar -c $__tool_directory__/snpEff/snpEff.config - -i vcf -upDownStreamLen 5000 $genome - $input > $__tool_directory__/tmp ; + -i vcf -upDownStreamLen 5000 $genome $input > $__tool_directory__/tmp_$input.name ; python $__tool_directory__/xenaHeader.py $snpeff_output; - cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output + cat $__tool_directory__/tmp_$input.name | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output; + rm $__tool_directory__/tmp_$input.name </command> <inputs> <param format="vcf" name="input" type="data" label="Input VCF file"/>