Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 61:0bab34a58764 draft

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Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 10:23:06 -0500
parents cb0f5c219244
children 34b5f8c5c16e
files varscan_mpileup2snp.xml
diffstat 1 files changed, 2 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_mpileup2snp.xml	Wed Mar 05 10:10:54 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 10:23:06 2014 -0500
@@ -23,9 +23,7 @@
 		#end if
 		
 		#if $varscan_output_vcf
-			 --output-vcf 0 
-		#else
-			--output-vcf 0 
+			 --output-vcf 1 
 		#end if
 		
 		 2> stderr.txt 
@@ -34,7 +32,7 @@
 	</command>
 	
 	<inputs>
-		<param format="mpileup,pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/>
+		<param format="mpileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/>
 		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">