Mercurial > repos > jampradinuk > repo_testing
view fastq_paired_reads_convention.xml @ 6:84889c68396d draft default tip
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author | jampradinuk |
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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>