Mercurial > repos > melissacline > ucsc_cancer_utilities

diff 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
line wrap: on
line diff
--- a/vcfToXena.xml	Thu Aug 13 23:26:33 2015 -0700
+++ b/vcfToXena.xml	Fri Aug 14 00:04:41 2015 -0700
@@ -4,7 +4,8 @@
       java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar  -c $__tool_directory__/snpEff/snpEff.config 
       -i vcf -upDownStreamLen 5000 $genome
       $input > $__tool_directory__/tmp ;
-      cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py  $input.name $snpeff_output
+      python $__tool_directory__/xenaHeader.py $snpeff_output;
+      cat $__tool_directory__/tmp | python $__tool_directory__/parseSnpEffVcf.py $input.name $snpeff_output
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Input VCF file"/>