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1 <?xml version="1.0"?>
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2 <tool id="ipcress_gff" name="IPCRESS to GFF">
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3 <description>Convert output from In-Silico PCR Experiment Simulation System to GFF format</description>
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4 <command>
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5 awk '/^ipcress:/, split($2,HIT,":"){print HIT[1],$3,$4,$5,$6,$7,$8,$9,$10,$11}' $input1 | awk -v OFS='\t' '{print $1,"ipcress","PCR_product",$5,$8,".","+",".","Name="$2}' > $output1
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6 </command>
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7 <inputs>
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8 <param format="txt" name="input1" type="data" label="iPCRESS ouptut" />
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9 </inputs>
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10 <outputs>
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11 <data format="gff" name="output1" />
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input1" value="ipcress.out" ftype="txt" />
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16 <output name="output1" file="ipcress_gff.out" />
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17 </test>
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18 </tests>
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19 <help>
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20 Uses awk to parse IPCRESS output to gff file format
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21 </help>
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22 </tool>
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