--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/getExons.xml	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,72 @@
+<tool id="getExons" name="get exons">
+    <description>Get the exons of a set of transcripts.</description>
+    <command interpreter="python">
+		../Java/Python/getExons.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
+		
+		#if $optionSelect.Value == "Yes":
+			-s $optionSelect.selectValue
+		#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>
+
+		<conditional name="optionSelect">
+			<param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')">
+				<option value="Yes">Yes</option>
+				<option value="No" selected="true">No</option>
+			</param>
+			<when value="Yes">
+				<param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/>
+			</when>
+			<when value="No">
+			</when>
+		</conditional>
+    </inputs>
+        
+    <outputs>
+        <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/>       
+    </outputs> 
+</tool>