Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 53:77578b1e98e4 draft

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Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 09:36:09 -0500
parents b2dc8ab51a79
children 8d1ddd8eb2b5
files varscan_mpileup2snp.xml
diffstat 1 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_mpileup2snp.xml	Wed Mar 05 09:18:21 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 09:36:09 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from mpileup file(s)">
-	<description>VarScan2 SNP/SNV detection; directly reading *.mpileup file(s).</description>
+<tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file">
+	<description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description>
 	<requirements>
 		<requirement type="package" version="2.3.6">VarScan</requirement>
 	</requirements>
@@ -23,8 +23,9 @@
 		#end if
 		
 		 --output-vcf $varscan_output_vcf
-		 > $snv_output
-		 2> &amp;1
+		 2> stderr.txt 
+		 > $snv_output ;
+		 cat stderr.txt
 	</command>
 	
 	<inputs>