Mercurial > repos > jampradinuk > repo_testing
changeset 3:f07f9188fcdb draft
Uploaded
| author | jampradinuk |
|---|---|
| date | Thu, 10 May 2012 16:36:55 -0400 |
| parents | 50905eb47f2d |
| children | a8eccdcc0800 |
| files | fastq_paired_reads_convention.xml |
| diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /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>