# HG changeset patch
# User serranop
# Date 1379102144 14400
# Node ID eec0db6ca4193048f2910fee783412b82bd23f4d
# Parent  3a85f43cfa4b26148314f3a66f1ab27c001d04f1
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diff -r 3a85f43cfa4b -r eec0db6ca419 usearch_fastq_mergepairs.xml
--- a/usearch_fastq_mergepairs.xml	Fri Sep 13 15:44:19 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Fri Sep 13 15:55:44 2013 -0400
@@ -1,7 +1,10 @@
 <tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.1">
     <description>merging of paired reads</description>
     <version_command>usearch -version</version_command>
-    <command>usearch
+    <command interpreter='bash'>usearch_wrapper.sh
+usearch
+-fastq_minovlen 0
+-quiet
 -fastq_mergepairs '$input_forward'
 -reverse '$input_reverse'
 #if $minovlen != '0':
diff -r 3a85f43cfa4b -r eec0db6ca419 usearch_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/usearch_wrapper.sh	Fri Sep 13 15:55:44 2013 -0400
@@ -0,0 +1,9 @@
+#!/bin/bash
+echo "$*"
+OUTPUT=`$* 2>&1`
+if [ $? -ne 0 ]
+then
+    echo "ERROR: $OUTPUT" 1>&2
+    exit
+fi
+echo $OUTPUT