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6
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1 <tool id="cleanGff" name="clean Gff">
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15
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2 <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description>
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6
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3 <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile
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4 -t $type
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5 -o $outputFile
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6 </command>
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7
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8 <inputs>
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9 <param name="inputFile" type="data" label="Input File" format="gff"/>
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15
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10 <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/>
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6
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11 </inputs>
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12
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13 <outputs>
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14 <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
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15 </outputs>
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16
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15
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17 <help>
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18 A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column).
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19 </help>
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6
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20 </tool>
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21
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