Mercurial > repos > yufei-luo > s_mart

annotate SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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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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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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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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16 <help>
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17 Note that iputs files should be sorted by increasing positions and that expressed referencies should be included in transcripts.
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19 Command example: perl splitTranscriptGff.pl -i annotations.gff -j transcripts.gff > TUTag.gff3
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20 </help>
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21 </tool>