Mercurial > repos > john-mccallum > pcr_markers
comparison patman.xml @ 1:a0689dc29b7f draft
Updated vcf to gff conversion tool
| author | john-mccallum |
|---|---|
| date | Tue, 31 Jul 2012 00:33:11 -0400 |
| parents | 21053f7f9ed1 |
| children |
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| 0:21053f7f9ed1 | 1:a0689dc29b7f |
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| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="patman_1" name="search for patterns in DNA using PatMaN"> | 2 <tool id="patman_1" name="search for patterns in DNA using PatMaN"> |
| 3 <description>search for approximate patterns in DNA libraries</description> | 3 <description>search for approximate patterns in DNA libraries</description> |
| 4 <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command> | 4 <command>patman -a -e $edits -g $gaps -D $inputfastaFile -P $inputPatfile | sort | uniq > $patman_outputfile </command> |
| 5 <inputs> | 5 <inputs> |
| 6 <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" /> | 6 <param name="edits" type="integer" label="max N mismatches and or gaps" value="0" size="1" /> |
| 7 <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/> | 7 <param name="gaps" type="integer" label="max N gaps" value="0" size="1"/> |
| 8 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" /> | 8 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta target file" /> |
| 9 <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" /> | 9 <param format="fasta" name="inputPatfile" type="data" label="Pattern fasta" /> |