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