Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 55:3296b5c8a968 draft

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Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 09:49:32 -0500
parents 8d1ddd8eb2b5
children 62219bff4fbf
files samtools-parallel-mpileup.xml
diffstat 1 files changed, 12 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/samtools-parallel-mpileup.xml	Wed Mar 05 09:39:25 2014 -0500
+++ b/samtools-parallel-mpileup.xml	Wed Mar 05 09:49:32 2014 -0500
@@ -66,9 +66,11 @@
 			#end for
 			
 			 2> stderr_1.txt
-			#if $sort_mpileup == "true"
+			
+			#if $sort_mpileup
 			 | sort -k 1,1 -k 2,2 
 			#end if
+			
 			 > $output ;
 			 cat stderr_1.txt
 		#end if
@@ -183,36 +185,27 @@
 	<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" />
 			
 			
 			<output name="output" file="hg19_mutant.mpileup" /> 
 		</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" />
 			
 			
 			<output name="output" file="hg19_mutant.mpileup" />