<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>