Mercurial > repos > clairetn > detrprok_scripts

diff detrprok_scripts/splitTranscriptGff.xml @ 0:a53eb951b164 draft

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author clairetn
date Mon, 25 Mar 2013 05:39:29 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/detrprok_scripts/splitTranscriptGff.xml	Mon Mar 25 05:39:29 2013 -0400
@@ -0,0 +1,27 @@
+<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 referencies should be included in transcripts.
+	</help>
+</tool>