# HG changeset patch
# User yhoogstrate
# Date 1394030169 18000
# Node ID 77578b1e98e495778dbf71c329c0a9941bff8716
# Parent  b2dc8ab51a79f3b39ae946cedbc2ad3b3db90fde
Uploaded

diff -r b2dc8ab51a79 -r 77578b1e98e4 varscan_mpileup2snp.xml
--- 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>