Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 63:38ea7a0450bc draft

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Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 10:52:11 -0500
parents 34b5f8c5c16e
children bafa6c859303
files varscan_mpileup2snp.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_mpileup2snp.xml	Wed Mar 05 10:23:12 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 10:52:11 2014 -0500
@@ -32,7 +32,7 @@
 	</command>
 	
 	<inputs>
-		<param format="mpileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/>
+		<param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? -->
 		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
@@ -66,7 +66,7 @@
 	
 	<tests>
 		<test>
-			<param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="mpileup" />
+			<param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" />
 			<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />