Mercurial > repos > john-mccallum > pcr_markers
comparison patman2gff.xml @ 0:21053f7f9ed1 draft
First upload of PCR Marker tools
| author | john-mccallum |
|---|---|
| date | Thu, 14 Jun 2012 19:29:26 -0400 |
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| -1:000000000000 | 0:21053f7f9ed1 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="patman2gff" name="convert patman to GFF3"> | |
| 3 <description>convert output of patman pattern detection to gvf/gff3</description> | |
| 4 <command>awk 'OFS="\t" {print $1,"patman","primer_binding_site",$3,$4,$6,$5,".","name="$2}' $inputFile > $outputfile</command> | |
| 5 <inputs> | |
| 6 <param format="tabular" name="inputFile" type="data" label="Input patman File" help="tabular output from patman tool" /> | |
| 7 </inputs> | |
| 8 <outputs> | |
| 9 <data format="gff3" name="outputfile" /> | |
| 10 | |
| 11 </outputs> | |
| 12 <help> | |
| 13 This tool provides a simple conversion from patman column output to GFF3 | |
| 14 | |
| 15 ------------------------------- | |
| 16 | |
| 17 *If you use this tool please cite:* | |
| 18 | |
| 19 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: | |
| 20 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.) | |
| 21 (2012) | |
| 22 | |
| 23 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, | |
| 24 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum | |
| 25 </help> | |
| 26 </tool> |