# HG changeset patch
# User stheil
# Date 1444983379 14400
# Node ID edda44d54b59fede62560daf2a4eb329a2636b7d
# Parent  14f74ce39bb1c29eb27c53c4a82a6636a31f6486
Uploaded

diff -r 14f74ce39bb1 -r edda44d54b59 fq2fa.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fq2fa.xml	Fri Oct 16 04:16:19 2015 -0400
@@ -0,0 +1,55 @@
+<tool id="fq2fa" name="fq2fa" version="1.1.1 (Oct 18, 2012)">
+  <description>fq2fa is a simple tool given by IDBA package that allows to convert fastq to fasta, merge paired-end reads and filter out reads containing 'N's</description>
+  <command>
+    fq2fa
+    #if $fileLayout.layout=='paired'
+      --paired $fileLayout.sequence
+    #else if $fileLayout.layout=='merge'
+      --merge $fileLayout.sequenceR1 $fileLayout.sequenceR2
+    #else
+      $fileLayout.sequence
+    #end if
+    $filter
+    $output
+  </command>
+  <inputs>
+    <conditional name="fileLayout">
+      <param name="layout" type="select" label="File layout">
+        <option value="">single end</option>
+        <option value="paired">paired-end in one file</option>
+        <option value="merge">paired-end in two files</option>
+      </param>
+      <when value="">
+        <param name="sequence" type="data" format="fastq" label="Single sequence file"/>
+      </when>
+      <when value="--paired">
+        <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/>
+      </when>
+      <when value="--merge">
+        <param name="sequenceR1" type="data" format="fastq" label="Forward sequence file (R1)"/>
+        <param name="sequenceR2" type="data" format="fastq" label="Reverse sequence file (R2)"/>
+      </when>
+    </conditional>
+    <param name="filter" type="boolean" checked="false" truevalue="--filter" falsevalue="" label="Filter out reads containing 'N'"/>
+  </inputs>
+  <outputs>
+		<data name="output" format="fasta" label="Fasta from fq2fa"/>
+	</outputs>
+  <help>
+=====
+fq2fa
+=====
+Convert Fastq sequences to Fasta sequences.
+
+| ``Usage:``
+| ``fq2fa tmp.fq tmp.fa [...]``
+| ``fq2fa --paired tmp.fq tmp.fa``
+| ``fq2fa --merge tmp_1.fq tmp_2.fq tmp.fa``
+|
+| Allowed Options:
+
+--paired  if the reads are paired-end in one file
+--merge   if the reads are paired-end in two files
+--filter  filter out reads containing 'N'
+  </help>
+</tool>