--- a/SMART/galaxy/Clusterize.xml	Mon Feb 10 03:39:09 2014 -0500
+++ b/SMART/galaxy/Clusterize.xml	Fri Feb 21 08:32:36 2014 -0500
@@ -4,26 +4,8 @@
 		<requirement type="set_environment">PYTHONPATH</requirement>
 	</requirements>
 	<command interpreter="python">
-		../Java/Python/clusterize.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 == 'bam':
-			-f bam
-		#elif $formatType.FormatInputFileName == 'gtf':
-			-f gtf
-		#end if
-		-o $outputFileGff 
-		$colinear
-		$normalize
-		-d $distance
+		#set $inputFiles = ",".join(["%s" % (s) for s in $formatType.inputFileName])
+		../Java/Python/clusterize.py -i $inputFiles -f $formatType.FormatInputFileName -o $outputFileGff $colinear $normalize -d $distance
 	</command>
 
 	<inputs>
@@ -34,29 +16,29 @@
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
 				<option value="sam">sam</option>
+				<option value="gtf">gtf</option>
 				<option value="bam">bam</option>
-				<option value="gtf">gtf</option>
 			</param>
 			<when value="bed">
-				<param name="inputFileName" format="bed" type="data" label="Input File"/>
+				<param name="inputFileName" format="bed" type="data" multiple="true" label="Input File"/>
 			</when>
 			<when value="gff">
-				<param name="inputFileName" format="gff" type="data" label="Input File"/>
+				<param name="inputFileName" format="gff" type="data" multiple="true" label="Input File"/>
 			</when>
 			<when value="gff2">
-				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
+				<param name="inputFileName" format="gff2" type="data" multiple="true" label="Input File"/>
 			</when>
 			<when value="gff3">
-				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
+				<param name="inputFileName" format="gff3" type="data" multiple="true" label="Input File"/>
 			</when>
 			<when value="sam">
-				<param name="inputFileName" format="sam" type="data" label="Input File"/>
+				<param name="inputFileName" format="sam" type="data" multiple="true" label="Input File"/>
+			</when>
+			<when value="gtf">
+				<param name="inputFileName" format="gtf" type="data" multiple="true" label="Input File"/>
 			</when>
 			<when value="bam">
-				<param name="inputFileName" format="bam" type="data" label="Input File"/>
-			</when>
-			<when value="gtf">
-				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
+				<param name="inputFileName" format="bam" type="data" multiple="true" label="Input File"/>
 			</when>
 		</conditional>