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author jampradinuk
date Thu, 10 May 2012 17:19:35 -0400
parents f07f9188fcdb
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<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>