# HG changeset patch
# User yhoogstrate
# Date 1394029101 18000
# Node ID b2dc8ab51a79f3b39ae946cedbc2ad3b3db90fde
# Parent  11292b6c3c6c785b923bd361acd82d370555a8b1
Uploaded

diff -r 11292b6c3c6c -r b2dc8ab51a79 samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Wed Mar 05 08:47:37 2014 -0500
+++ b/samtools-parallel-mpileup.xml	Wed Mar 05 09:18:21 2014 -0500
@@ -183,27 +183,36 @@
 	<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="extended_parameters_regions.samtools_regions" value="entire_genome" />
+			<!-- <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="mpileup_parallelization.mpileup_parallelization_select" value="false" />
+			<!-- <param name="mpileup_parallelization.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="extended_parameters.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="extended_parameters_regions.samtools_regions" value="entire_genome" />
+			<!-- <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="mpileup_parallelization.mpileup_parallelization_select" value="true" />
-			<param name="mpileup_parallelization.samtools_threads" value="2" />
+			<!-- <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="sort_mpileup" value="true" />
 			
-			<param name="extended_parameters.parameters" value="default" />
+			<!-- <param name="extended_parameters.parameters" value="default" /> -->
+				<param name="parameters" value="default" />
 			
 			
 			<output name="output" file="hg19_mutant.mpileup" /> 
diff -r 11292b6c3c6c -r b2dc8ab51a79 varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Wed Mar 05 08:47:37 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 09:18:21 2014 -0500
@@ -63,7 +63,10 @@
 	<tests>
 		<test>
 			<param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="bam" />
-			<param name="extended_parameters.parameters" value="default" />
+			
+			<!-- <param name="extended_parameters.parameters" value="default" /> -->
+				<param name="parameters" value="default" />
+			
 			<param name="varscan_output_vcf" value="1" />
 			
 			<output name="snv_output" file="hg19_mutant.vcf" />
diff -r 11292b6c3c6c -r b2dc8ab51a79 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 08:47:37 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 09:18:21 2014 -0500
@@ -226,13 +226,17 @@
 	<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="extended_parameters_regions.samtools_regions" value="entire_genome" />
+			<!-- <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="mpileup_parallelization.mpileup_parallelization_select" value="false" />
+			<!-- <param name="mpileup_parallelization.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="extended_parameters.parameters" value="default" /> -->
+				<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />
 			
 			
@@ -240,14 +244,19 @@
 		</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="extended_parameters_regions.samtools_regions" value="entire_genome" />
+			<!-- <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="mpileup_parallelization.mpileup_parallelization_select" value="true" />
-			<param name="mpileup_parallelization.samtools_threads" value="2" />
+			<!-- <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="sort_mpileup" value="true" />
 			
-			<param name="extended_parameters.parameters" value="default" />
+			<!-- <param name="extended_parameters.parameters" value="default" /> -->
+				<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />