--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/getIntrons.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,71 @@
+<tool id="getIntrons" name="get introns">
+    <description>Get the introns of a set of transcripts.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+    <command interpreter="python">
+		../Java/Python/getIntrons.py -i $formatType.inputFileName
+		#if $formatType.FormatInputFileName == 'bed':
+			-f bed
+		#elif $formatType.FormatInputFileName == 'gff':
+			-f gff
+		#elif $formatType.FormatInputFileName == 'gff2':
+			-f gff2
+		#elif $formatType.FormatInputFileName == 'gff3':
+			-f gff3
+		#elif $formatType.FormatInputFileName == 'sam':
+			-f sam
+		#elif $formatType.FormatInputFileName == 'gtf':
+			-f gtf
+		#end if
+		-o $outputFileGff 
+	</command>
+	
+    <inputs>
+		<conditional name="formatType">
+			<param name="FormatInputFileName" type="select" label="Input 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"/>
+			</when>
+			<when value="gff">
+				<param name="inputFileName" format="gff" type="data" label="Input File"/>
+			</when>
+			<when value="gff2">
+				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
+			</when>
+			<when value="gff3">
+				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
+			</when>
+			<when value="sam">
+				<param name="inputFileName" format="sam" type="data" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
+			</when>
+		</conditional>
+
+    </inputs>
+        
+    <outputs>
+        <data format="gff3" name="outputFileGff" label="[get introns] output file"/>       
+    </outputs> 
+<tests>
+    <test>
+      <param name="FormatInputFileName" value="gtf" />
+      <param name="inputFileName" value="genes.gtf" />
+      <output name="outputFileGff" file="exp_getIntrons.gff3" />
+    </test>
+  </tests>
+
+	<help>
+Provide all the introns of an annotation file.
+	</help>
+
+</tool>