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1 <tool id="changeGffFeatures" name="change GFF features">
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15
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2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description>
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18
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6
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6 <command interpreter="bash">
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7 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
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8 </command>
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9 <inputs>
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10 <param name="inputFile" type="data" label="Input File" format="gff"/>
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11 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/>
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12 <param name="outputFeature" type="text" value="exon" label="The new feature"/>
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6
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13 </inputs>
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14
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15 <outputs>
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16 <data name="outputFile" format="gff" label="[change GFF features] Output File"/>
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6
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17 </outputs>
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18
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19 <help>
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20 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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21 </help>
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6
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22 </tool>
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23
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