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1 <tool id="changeGffFeatures" name="change gff Features">
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2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description>
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3 <command interpreter="bash">
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4 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
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5 </command>
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6 <inputs>
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7 <param name="inputFile" type="data" label="Input File" format="gff"/>
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8 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/>
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9 <param name="outputFeature" type="text" value="exon" label="The new feature"/>
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10 </inputs>
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12 <outputs>
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13 <data name="outputFile" format="gff" label="[changeGffFeatures] Output File"/>
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14 </outputs>
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15
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16 <help>
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17 This script changes the third column of a GFF3 file (please refer to http://www.sequenceontology.org/gff3.shtml to know more about this format).
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18 </help>
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19 </tool>
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