Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml	Tue Apr 30 14:33:21 2013 -0400
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+<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>