diff vcfToXena.xml @ 47:23d98125d20c

parse snpEff output

--- a/vcfToXena.xml	Thu Aug 13 21:49:03 2015 -0700
+++ b/vcfToXena.xml	Thu Aug 13 23:26:33 2015 -0700
@@ -1,9 +1,10 @@
 <tool id="vcfToXena" name="vcfToXena" version="0.1">
-    <description>Vcf To Xena positional mutation data</description>
+    <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 > $snpeff_output 
+      $input > $__tool_directory__/tmp ;
+      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"/>
@@ -13,7 +14,7 @@
 
     </inputs>
     <outputs>
-        <data format="vcf" name="snpeff_output" />
+        <data format="tabular" name="snpeff_output" label="${input.name}.mutationVector" />
     </outputs>
     <help>
       This tool convert vcf files to xena ready positional mutation data files.