--- a/SMART/galaxy/clusterize.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/clusterize.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
 <tool id="MergingDataClusterize" name="Clusterize">
-	<description>Clusterizes the reads when their genomic intervals overlap.</description>
+	<description>Clusterize features when their genomic intervals overlap.</description>
 	<command interpreter="python">
 		../Java/Python/clusterize.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
@@ -10,8 +10,6 @@
 			-f gff2
 		#elif $formatType.FormatInputFileName == 'gff3':
 			-f gff3
-		#elif $formatType.FormatInputFileName == 'csv':
-			-f csv
 		#elif $formatType.FormatInputFileName == 'sam':
 			-f sam
 		#end if
@@ -29,7 +27,6 @@
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
-				<option value="csv">csv</option>
 				<option value="sam">sam</option>
 			</param>
 			<when value="bed">
@@ -44,24 +41,17 @@
 			<when value="gff3">
 				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
 			</when>
-			<when value="csv">
-				<param name="inputFileName" format="csv" type="data" label="Input File"/>
-			</when>
 			<when value="sam">
 				<param name="inputFileName" format="sam" type="data" label="Input File"/>
 			</when>
 		</conditional>
 
-		<param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/>
-		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (attention!! Only for GFF3 file!!!!!)"/>
-		<param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/>
-		<param name="distance" type="integer" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
+		<param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/>
+		<param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/>
+		<param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/>
 	</inputs>
 
 	<outputs>
 		<data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
-		<data name="outputFileLog" format="txt" label="[clusterize]output file">
-			<filter>log</filter>
-		</data>
 	</outputs> 
 </tool>