<?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>