# HG changeset patch
# User yhoogstrate
# Date 1394030986 18000
# Node ID 83d480908f4b262f0f248fc0bf74a0ee45cad100
# Parent  62219bff4fbf0a5d2720684ddd6e48ced3e7a9fe
Uploaded

diff -r 62219bff4fbf -r 83d480908f4b varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 09:49:39 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 09:49:46 2014 -0500
@@ -84,10 +84,13 @@
 			#end if
 			
 			 --output-vcf $varscan_output_vcf
+			
 			 2> stderr_2.txt 
-			#if $sort_mpileup == "true"
+			
+			#if $sort_mpileup
 			 | sort -k 1,1 -k 2,2 
 			#end if
+			
 			 > $snv_output ;
 			 
 			 echo "-------------------------[ mpileup generation ]-------------------------" ;
@@ -227,17 +230,13 @@
 	<tests>
 		<test><!-- Use classical samtools -->
 			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" />
-			<!-- <param name="reference_genome_source.source_select" value="attribute" /> -->
-				<param name="source_select" value="attribute" />
-			<!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> -->
-				<param name="samtools_regions" value="entire_genome" />
+			<param name="source_select" value="attribute" />
+			<param name="samtools_regions" value="entire_genome" />
 			
-			<!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> -->
-				<param name="mpileup_parallelization_select" value="false" />
+			<param name="mpileup_parallelization_select" value="false" />
 			<param name="sort_mpileup" value="true" />
 			
-			<!-- <param name="extended_parameters.parameters" value="default" /> -->
-				<param name="parameters" value="default" />
+			<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />
 			
 			
@@ -245,19 +244,14 @@
 		</test>
 		<test><!-- Use parallelized samtools -->
 			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" />
-			<!-- <param name="reference_genome_source.source_select" value="attribute" /> -->
-				<param name="source_select" value="attribute" />
-			<!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> -->
-				<param name="samtools_regions" value="entire_genome" />
+			<param name="source_select" value="attribute" />
+			<param name="samtools_regions" value="entire_genome" />
 			
-			<!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> -->
-				<param name="mpileup_parallelization_select" value="true" />
-			<!-- <param name="mpileup_parallelization.samtools_threads" value="2" /> -->
-				<param name="samtools_threads" value="2" />
+			<param name="mpileup_parallelization_select" value="true" />
+			<param name="samtools_threads" value="2" />
 			<param name="sort_mpileup" value="true" />
 			
-			<!-- <param name="extended_parameters.parameters" value="default" /> -->
-				<param name="parameters" value="default" />
+			<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />