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diff patman2gff.xml @ 0:21053f7f9ed1 draft

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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/patman2gff.xml	Thu Jun 14 19:29:26 2012 -0400
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+<?xml version="1.0"?>
+<tool id="patman2gff" name="convert patman to GFF3">
+  <description>convert output of patman pattern detection to gvf/gff3</description>
+  <command>awk 'OFS="\t" {print $1,"patman","primer_binding_site",$3,$4,$6,$5,".","name="$2}' $inputFile  >  $outputfile</command>
+  <inputs>
+    <param format="tabular" name="inputFile" type="data" label="Input patman File" help="tabular output from patman tool" />
+  </inputs>
+  <outputs>
+<data format="gff3" name="outputfile" />
+
+  </outputs>
+<help>
+This tool provides a simple conversion from patman column output to GFF3
+
+-------------------------------
+
+*If you use this tool please cite:*
+
+A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
+Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
+(2012)
+
+Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
+Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
+</help>
+</tool>