Mercurial > repos > cwallon > split_transcript

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

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author cwallon
date Fri, 01 Mar 2013 11:44:48 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SplitTranscript/splitTranscriptGff.xml	Fri Mar 01 11:44:48 2013 -0500
@@ -0,0 +1,29 @@
+<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>