# HG changeset patch
# User serranop
# Date 1379097730 14400
# Node ID 94cda55f1bbb4bec7b940b8922893759554e4867
# Parent  d0974e1ff717669171ba259c3a0a5e452fdcc6ec
Added -fastq_minovlen option

diff -r d0974e1ff717 -r 94cda55f1bbb usearch_fastq_mergepairs.xml
--- a/usearch_fastq_mergepairs.xml	Fri Sep 13 14:13:31 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Fri Sep 13 14:42:10 2013 -0400
@@ -2,16 +2,20 @@
     <description>merging of paired reads</description>
     <version_command>usearch -version</version_command>
     <command>usearch
-		-quiet
-        -fastq_mergepairs '$input_forward'
-        -reverse '$input_reverse'
-        -fastq_qmax $qmax
-        -fastqout '$output'
+-quiet
+-fastq_mergepairs '$input_forward'
+-reverse '$input_reverse'
+#if $minovlen != '-1':
+-fastq_minovlen $minovlen
+#end if
+-fastq_qmax $qmax
+-fastqout '$output'
     </command>
     <inputs>
-        <param name='input_forward' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the forward reads' />
-        <param name='input_reverse' type='data' format='fastq,fastqsanger,fastqcssanger' label='The FASTQ filename for the reverse reads' />
-        <param name='qmax' type='integer' value='41' label='Maximum Q score (input files).' />
+        <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" />
+        <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" />
+        <param name="minovlen" type="integer" value="-1" label="Minimum length of the overlap" help="'-1' means no minimum." />
+        <param name="qmax" type="integer" value="41" label="Maximum Q score (input files)." />
     </inputs>
     <outputs>
         <data name='output' format='fastq' label="Merge result" />