# HG changeset patch
# User jingchunzhu
# Date 1439536675 25200
# Node ID 986bca7bc318f41fd5352ba2e5c20f5ce859b2df
# Parent  a38cc72edd75c031869c552a56dee830f5249fb7
multiple files

diff -r a38cc72edd75 -r 986bca7bc318 vcfToXena.xml
--- 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"/>