Mercurial > repos > jampradinuk > repo_testing
comparison 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 |
children |
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5:f87183778470 | 6:84889c68396d |
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1 <tool id="FASTQPairedReadsConvention" name="Convert paired reads format"> | |
2 <description>to conventional (/1 and /2)</description> | |
3 <command interpreter="perl">fastq_paired_reads_convention.pl $input $left_out $right_out</command> | |
4 <inputs> | |
5 <param name="input" type="data" label="FASTQ file" format="fastqsanger, fastqcssanger"></param></inputs> | |
6 <outputs> | |
7 <data format="input" name="left_out"></data> | |
8 <data format="input" name="right_out"></data></outputs> | |
9 <help> | |
10 | |
11 **What it does** | |
12 | |
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). | |
14 | |
15 ----- | |
16 | |
17 **Example** | |
18 | |
19 Data like this:: | |
20 | |
21 <![CDATA[ | |
22 @M00325:2:000000000-A0DG1:1:1:15761:1554 1:N:0:1 | |
23 NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG | |
24 + | |
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&(+(&)&&&)(&((((((((+(&&((+++(((+((& | |
26 ]]> | |
27 | |
28 will produce an empty right file and a left file with one entry like this:: | |
29 | |
30 <![CDATA[ | |
31 @M00325:2:000000000-A0DG1:1:1:15761:1554/1 | |
32 NAACGCGCCCACACAGCTGTGGTTGGGGCGCCCGCTGATCGGTGATGGCGTTCACGGGGCGCCGGGGACCGGGCAGCCCGGTGGGGCCGGGGGGTTGTTGTGGGGTAATGGCGGTAACGGCGGTTCGTTGGCTGCCCGTCACTTCTGTGGG | |
33 +M00325:2:000000000-A0DG1:1:1:15761:1554/1 | |
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&(+(&)&&&)(&((((((((+(&&((+++(((+((& | |
35 ]]> | |
36 | |
37 </help></tool> |