# HG changeset patch
# User yhoogstrate
# Date 1402575953 14400
# Node ID bf44ae0d9264d3e5995a486f3eeca87ec98b82a2
# Parent  404583a3d754c157f0cd3ba12fe8f6e65a545804
Uploaded

diff -r 404583a3d754 -r bf44ae0d9264 test-data/GSM1244820_Control_Rep5.hg18.subset.bam
Binary file test-data/GSM1244820_Control_Rep5.hg18.subset.bam has changed
diff -r 404583a3d754 -r bf44ae0d9264 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 11 05:57:04 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 12 08:25:53 2014 -0400
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	
+	<!--
 	<package name="ncurses" version="5.9">
 		<repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 	</package>
+	-->
 	
 	<package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a">
 		<install version="1.0">
@@ -40,12 +42,6 @@
 		</readme>
 	</package>
 	
-	<!--
-	<package name="package_samtools_0_1_19" version="0.1.19">
-		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-	</package>
-	-->
-	
 	<package name="ncurses" version="5.9">
 		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 	</package>
diff -r 404583a3d754 -r bf44ae0d9264 varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Wed Jun 11 05:57:04 2014 -0400
+++ b/varscan_mpileup2snp.xml	Thu Jun 12 08:25:53 2014 -0400
@@ -6,19 +6,19 @@
 	</requirements>
 	<command>
 		cat $mpileup_input | java
-				 -Xmx64G
-				 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
-					 mpileup2snp
+			 -Xmx64G
+			 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
+				 mpileup2snp
 		 
 		#if $extended_parameters.parameters == "extended"
-				 --min-coverage	 $varscan_min_coverage
-				 --min-reads2	   $varscan_min_reads2
-				 --min-avg-qual	 $varscan_min_avg_qual
-				 --min-var-freq	 $varscan_min_var_freq
-				 --min-freq-for-hom $varscan_min_freq_for_hom
-				 --p-value		  $varscan_p_value
-				 $varscan_strand_filter 
-				 $varscan_variants 
+			 --min-coverage     $extended_parameters.varscan_min_coverage
+			 --min-reads2       $extended_parameters.varscan_min_reads2
+			 --min-avg-qual     $extended_parameters.varscan_min_avg_qual
+			 --min-var-freq     $extended_parameters.varscan_min_var_freq
+			 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+			 --p-value          $extended_parameters.varscan_p_value
+			                    $extended_parameters.varscan_strand_filter 
+			                    $extended_parameters.varscan_variants 
 		#end if
 		
 		#if $varscan_output == "vcf" or $varscan_output.value == "vcf"
diff -r 404583a3d754 -r bf44ae0d9264 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Jun 11 05:57:04 2014 -0400
+++ b/varscan_mpileup2snp_from_bam.xml	Thu Jun 12 08:25:53 2014 -0400
@@ -14,6 +14,7 @@
 		#else
 			#import os.path
 			#for $alignment in $alignments
+				<!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] -->
 				#if not os.path.isfile(str($alignment)+".bai")
 				 echo "- Indexing alignment file: $alignment.name " ; 
 				 samtools index $alignment 2>&amp;1 ; 
@@ -91,14 +92,14 @@
 						 mpileup2snp
 			 
 			#if $extended_parameters.parameters == "extended"
-					 --min-coverage	 $varscan_min_coverage
-					 --min-reads2	   $varscan_min_reads2
-					 --min-avg-qual	 $varscan_min_avg_qual
-					 --min-var-freq	 $varscan_min_var_freq
-					 --min-freq-for-hom $varscan_min_freq_for_hom
-					 --p-value		  $varscan_p_value
-					 $varscan_strand_filter 
-					 $varscan_variants 
+					 --min-coverage     $extended_parameters.varscan_min_coverage
+					 --min-reads2       $extended_parameters.varscan_min_reads2
+					 --min-avg-qual     $extended_parameters.varscan_min_avg_qual
+					 --min-var-freq     $extended_parameters.varscan_min_var_freq
+					 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
+					 --p-value          $extended_parameters.varscan_p_value
+					                    $extended_parameters.varscan_strand_filter 
+					                    $extended_parameters.varscan_variants 
 			#end if
 			
 			#if $varscan_output == "vcf" or $varscan_output.value == "vcf"
@@ -108,17 +109,14 @@
 			 2>stderr_2.txt 
 			 > $snv_output ;
 			 
-			 echo "-------------------------[ mpileup generation ]-------------------------" ;
-			 echo "" ;
+			 
+			 echo "---------------[ mpileup generation ]---------------" ;
 			 cat stderr_1.txt ;
 			 echo "" ;
-			 echo "" ;
-			 echo "-------------------------[ VarScan SNP detect ]-------------------------" ;
-			 echo "" ;
-			 echo "" ;
+			 echo "---------------[ VarScan SNP detect ]---------------" ;
 			 cat stderr_2.txt ;
 			 echo "" ;
-			 echo "------------------------------------------------------------------------" ;
+			 echo "----------------------------------------------------" ;
 		#end if
 	</command>