view SplitTranscript/splitTranscriptGff.xml @ 0:0153bf95965c draft default tip

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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>

        <tests>
                <test>
                        <param name="referenciesFile" value="SplitTranscript_Reference.gff" />
                        <param name="transcriptsFile" value="SplitTranscript_TranscriptionUnit.gff" />
                        <output name="outputFile" file="SplitTranscript_Result.gff" />
                </test>
        </tests>

	<help>
		Note that inputs 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 > split_UTR_CDS.gff3
	</help>
</tool>