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1 <tool id="splitTranscriptGff" name="splitTranscriptGff">
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2 <description> Define UTRs and intergenic operonic regions from a transcript file and following a reference file </description>
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3 <command interpreter="perl">
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4 splitTranscriptGff.pl -i $referenciesFile -j $transcriptsFile > $outputFile
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5 </command>
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6
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7 <inputs>
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8 <param name="referenciesFile" type="data" label="Referencies Input File" format="gff" />
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9 <param name="transcriptsFile" type="data" label="Transcripts Input File" format="gff" />
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10 </inputs>
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11
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12 <outputs>
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13 <data format="gff3" name="outputFile" label="[splitTranscript] Output File"/>
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14 </outputs>
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15
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16 <tests>
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17 <test>
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18 <param name="referenciesFile" value="SplitTranscript_Reference.gff" />
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19 <param name="transcriptsFile" value="SplitTranscript_TranscriptionUnit.gff" />
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20 <output name="outputFile" file="SplitTranscript_Result.gff" />
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21 </test>
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22 </tests>
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23
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24 <help>
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25 Note that inputs files should be sorted by increasing positions and that expressed referencies should be included in transcripts.
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26
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27 Command example: perl splitTranscriptGff.pl -i annotations.gff -j transcripts.gff > split_UTR_CDS.gff3
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28 </help>
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29 </tool>
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