diff SMART/galaxy/removeIntrons.xml @ 56:97aa2e42bfdf

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/removeIntrons.xml	Wed Feb 05 11:51:11 2014 -0500
@@ -0,0 +1,45 @@
+<tool id="removeIntrons" name="remove introns">
+  <description>Removes the introns of the transcript files.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+  <command interpreter="python"> ../Java/Python/RemoveExons.py -i $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile  </command>
+  <inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName1" type="select" label="query File Format">
+				<option value="bed">bed</option>
+				<option value="gff">gff</option>
+				<option value="gff2">gff2</option>
+				<option value="gff3">gff3</option>
+				<option value="sam">sam</option>
+				<option value="gtf">gtf</option>
+			</param>
+			<when value="bed">
+				<param name="inputFileName" format="bed" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName" format="gff" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File 1"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File 1"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File 1"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File 1"/>
+			</when>
+		</conditional>
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[remove introns] output file"/>
+  </outputs>
+
+  <help>
+	Simply remove the introns of the input file, thus getting the unmatured transcript.
+  </help>
+</tool>