Mercurial > repos > jampradinuk > repo_testing

annotate my_tools/fastq_paired_reads_convention.xml @ 0:ba3bec698d3a draft

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First upload.
author jampradinuk
date Thu, 10 May 2012 16:34:08 -0400
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1 <tool id="FASTQPairedReadsConvention" name="Convert paired reads format">
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2 <description>to conventional (/1 and /2)</description>
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3 <command interpreter="perl">fastq_paired_reads_convention.pl $input $left_out $right_out</command>
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4 <inputs>
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5 <param name="input" type="data" label="FASTQ file" format="fastqsanger, fastqcssanger"></param></inputs>
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6 <outputs>
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7 <data format="input" name="left_out"></data>
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8 <data format="input" name="right_out"></data></outputs>
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9 <help>
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10
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11 **What it does**
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12
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13 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).
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14
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15 -----
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16
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17 **Example**
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18
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19 Data like this::
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20
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21 <![CDATA[
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22 @M00325:2:000000000-A0DG1:1:1:15761:1554 1:N:0:1
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23 NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
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24 +
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25 #+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&(+(&)&&&)(&((((((((+(&&((+++(((+((&
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26 ]]>
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27
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28 will produce an empty right file and a left file with one entry like this::
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29
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30 <![CDATA[
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31 @M00325:2:000000000-A0DG1:1:1:15761:1554/1
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32 NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG
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33 +M00325:2:000000000-A0DG1:1:1:15761:1554/1
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34 #+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&(+(&)&&&)(&((((((((+(&&((+++(((+((&
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35 ]]>
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36
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37 </help></tool>