Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 56:62219bff4fbf draft

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Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 09:49:39 -0500
parents 3296b5c8a968
children 83d480908f4b
files varscan_mpileup2snp.xml
diffstat 1 files changed, 3 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_mpileup2snp.xml	Wed Mar 05 09:49:32 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 09:49:39 2014 -0500
@@ -29,7 +29,7 @@
 	</command>
 	
 	<inputs>
-		<param format="mpileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
+		<param format="mpileup,pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
 		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
@@ -64,11 +64,9 @@
 	<tests>
 		<test>
 			<param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="bam" />
+			<param name="parameters" value="default" />
+			<param name="varscan_output_vcf" value="1" />
 			
-			<!-- <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" />
 		</test>