# HG changeset patch
# User yhoogstrate
# Date 1394032986 18000
# Node ID 0bab34a58764b13880190369b01fac47ba5ad3a1
# Parent  cb0f5c219244d264972d85ff16df4c9be72b2e10
Uploaded

diff -r cb0f5c219244 -r 0bab34a58764 varscan_mpileup2snp.xml
--- 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.">