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changeset 12:eec0db6ca419 draft

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author serranop
date Fri, 13 Sep 2013 15:55:44 -0400
parents 3a85f43cfa4b
children ecf3ba958543
files usearch_fastq_mergepairs.xml usearch_wrapper.sh
diffstat 2 files changed, 13 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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 $minovlen != '0':
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/usearch_wrapper.sh	Fri Sep 13 15:55:44 2013 -0400
@@ -0,0 +1,9 @@
+#!/bin/bash
+echo "$*"
+OUTPUT=`$* 2>&1`
+if [ $? -ne 0 ]
+then
+    echo "ERROR: $OUTPUT" 1>&2
+    exit
+fi
+echo $OUTPUT