# HG changeset patch
# User jampradinuk
# Date 1336682215 14400
# Node ID f07f9188fcdbcc097d08336cbfb9f3429f4d9832
# Parent  50905eb47f2d4af671f43ac0193af5cb2daa092d
Uploaded

diff -r 50905eb47f2d -r f07f9188fcdb fastq_paired_reads_convention.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_paired_reads_convention.xml	Thu May 10 16:36:55 2012 -0400
@@ -0,0 +1,37 @@
+<tool id="FASTQPairedReadsConvention" name="Convert paired reads format">
+	<description>to conventional (/1 and /2)</description>
+	<command interpreter="perl">fastq_paired_reads_convention.pl $input $left_out $right_out</command>
+	<inputs>
+		<param name="input" type="data" label="FASTQ file" format="fastqsanger, fastqcssanger"></param></inputs>
+	<outputs>
+		<data format="input" name="left_out"></data>
+		<data format="input" name="right_out"></data></outputs>
+	<help>
+	
+	**What it does**
+	
+	This tool takes a paired ends fastq file (with the first format below) and produces a left and right fastq file (with the second format below).
+	
+	-----
+	
+	**Example**
+	
+	Data like this::
+	
+    <![CDATA[
+	@M00325:2:000000000-A0DG1:1:1:15761:1554 1:N:0:1
+	NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
+	+
+	#+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((&
+    ]]>
+	
+	will produce an empty right file and a left file with one entry like this::
+	
+    <![CDATA[
+	@M00325:2:000000000-A0DG1:1:1:15761:1554/1
+	NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
+	+M00325:2:000000000-A0DG1:1:1:15761:1554/1
+	#+14:A?DAD1<;EBD@C3C33:C0)))8'5::69=6';;;/58<>335'898(:0&&&0&070&&05085-55538<<-5>999-550--5&559>9<8<<(&&)&(+(((&&0&(+(&)&&&)(&((((((((+(&&((+++(((+((&
+    ]]>
+	
+	</help></tool>