# HG changeset patch
# User serranop
# Date 1379173044 14400
# Node ID a1731593bc94b7c2eb664834abe2fe85afa1f551
# Parent  acaab750b5fb1f7a7df3b6ad04ce87cbbd06ab52
Testing

diff -r acaab750b5fb -r a1731593bc94 usearch_fastq_mergepairs.xml
--- a/usearch_fastq_mergepairs.xml	Fri Sep 13 17:28:01 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Sat Sep 14 11:37:24 2013 -0400
@@ -9,48 +9,15 @@
 #if $minovlen.value != 0
     -fastq_minovlen $minovlen
 #end if
-#if $minmergelen.value != 0
-    -fastq_minmergelen $minmergelen
-#end if
-#if $maxmergelen.value != 0
-    -fastq_maxmergelen $maxmergelen
-#end if
-#if $maxdiffs.value != 0
-    -fastq_maxdiffs $maxdiffs
-#end if
-#if $truncqual.value != 0
-    -fastq_truncqual $truncqual
-#end if
-#if $minlen.value != 0
-    -fastq_minlen $minlen
-#end if
-$allowmergestagger
--fastq_ascii $ascii
--fastq_qmin $qmin
 -fastq_qmax $qmax
--fastq_qmaxout $qmaxout
-#if $output_format.format == "fastq"
-    -fastqout $output
-#else
-    -fastaout $output
-#end if
+-fastqout $output
     </command>
     <inputs>
         <!-- INPUT OPTIONS -->
         <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="0" label="Minimum length of the overlap" help="'0' means no minimum." />
-        <param name="minmergelen" type="integer" value="0" label="Minimum length of the merged read" help="'0' means no minimum." />
-        <param name="maxmergelen" type="integer" value="0" label="Maximum length of the merged read" help="'0' means no maximum." />
-        <param name="maxdiffs" type="integer" value="0" label="Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" />
-        <param name="truncqual" type="integer" value="0" label="Truncate the forward and reverse reads at the first Q<=q, if present. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to use ‑fastq_trunqual 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." help="'0' means no quality truncation." />
-        <param name="minlen" type="integer" value="0" label="Minimum length of the forward and reverse read, after truncating per ‑fastq_truncqual if applicable." help="'0' means no minimum." />
-        <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="Allow merge of a pair where the alignment is staggered like this: --FORWARD
-  REVERSE--" help="By default, pairs with staggered alignments are discarded." />
-        <param name="ascii" type="integer" value="33" label="ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" />
-        <param name="qmin" type="integer" value="0" label="Minimum Q score" />
         <param name="qmax" type="integer" value="41" label="Maximum Q score for input files" />
-        <param name="qmaxout" type="integer" value="41" label="Maximum Q score for output files" />
 
         <!-- OUTPUT OPTIONS -->
         <conditional name="output_format">
@@ -63,7 +30,7 @@
         </conditional>
    </inputs>
     <outputs>
-        <data name="output" format="${output_format.format}" label="Merge result" />
+        <data name="output" format="fastq" label="Merge result" />
     </outputs>
     <tests>
         <test>