# HG changeset patch
# User morinlab
# Date 1485564381 18000
# Node ID 4e6e20c9738bd39e80ab64b590f00e7dfa8d1ed1
# Parent  3ce78c04c7e5081cdd0003bcea30581c3c429186
Uploaded

diff -r 3ce78c04c7e5 -r 4e6e20c9738b strelka.xml
--- a/strelka.xml	Tue Oct 11 14:34:44 2016 -0400
+++ b/strelka.xml	Fri Jan 27 19:46:21 2017 -0500
@@ -6,7 +6,7 @@
         <import>citations.xml</import>
     </macros>    
     <requirements>
-	<requirement type="package" version="1.0.14">strelka</requirement>
+<requirement type="package" version="1.0.14">strelka</requirement>
     </requirements>
     <command detect_errors="aggressive">
 
@@ -98,14 +98,14 @@
         
     #else
 
-        cat ./strelkaAnalysis/results/all.somatic.snvs.vcf > $snvs;
-        cat ./strelkaAnalysis/results/all.somatic.indels.vcf > $indels; 
+        cat ./strelkaAnalysis/results/passed.somatic.snvs.vcf > $snvs;
+        cat ./strelkaAnalysis/results/padded.somatic.indels.vcf > $indels; 
 
     #end if
 
     </command>
     <inputs>
-	<conditional name="reference_source">
+<conditional name="reference_source">
             <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                 <option value="cached">Use a built-in genome</option>
                 <option value="history">Use a genome from the history</option>
@@ -161,8 +161,8 @@
         <test>
             <param name="normal" value="test.normal.bam"/>
             <param name="normal.metadata.bam_index" value="test.normal.bam.bai"/>
-	          <param name="tumour" value="test.tumour.bam"/>
-	          <param name="tumour.metadata.bam_index" value="test.tumour.bam.bai"/>
+          <param name="tumour" value="test.tumour.bam"/>
+          <param name="tumour.metadata.bam_index" value="test.tumour.bam.bai"/>
             <param name="reference_source.reference_source_selector" value="history"/>
             <param name="reference_source.ref_file" value="test.fa"/>
             <output name="snvs" ftype="vcf" file="all.somatic.snvs.vcf" lines_diff="2"/>