Mercurial > repos > yufei-luo > s_mart
diff SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,21 @@ +<tool id="splitTranscriptGff" name="splitTranscriptGff"> + <description> Define UTRs and intergenic operonic regions from a transcript file and following a reference file </description> + <command interpreter="perl"> + splitTranscriptGff.pl -i $referenciesFile -j $transcriptsFile > $outputFile + </command> + + <inputs> + <param name="referenciesFile" type="data" label="Referencies Input File" format="gff" /> + <param name="transcriptsFile" type="data" label="Transcripts Input File" format="gff" /> + </inputs> + + <outputs> + <data format="gff3" name="outputFile" label="[splitTranscript] Output File"/> + </outputs> + + <help> + Note that iputs files should be sorted by increasing positions and that expressed referencies should be included in transcripts. + + Command example: perl splitTranscriptGff.pl -i annotations.gff -j transcripts.gff > TUTag.gff3 + </help> +</tool>