--- a/SMART/galaxy/plotTranscriptList.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/plotTranscriptList.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
 <tool id="plotTranscriptList" name="plot transcript list">
 	<description>Plot some information from a list of transcripts. </description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
 	<command interpreter="python">
 		../Java/Python/plotTranscriptList.py  -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'gff':
@@ -29,7 +32,7 @@
 			-m $optionyLab.labVal
 		#end if	
 
-		$optionLog.log
+		$log
 		-s $shape
 		-b $bucket
 		
@@ -102,14 +105,12 @@
 			</when>
 		</conditional>	
 
-		<conditional name="optionLog">
-			<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
-					<option value="" selected="true">No</option>
-					<option value="-l x">log on the x-axis</option>
-					<option value="-l y">log on the y-axis</option>
-					<option value="-l xy">log on the x- and y-axis</option>
-			</param>
-		</conditional>	
+		<param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
+				<option value="" selected="true">No</option>
+				<option value="-l x">log on the x-axis</option>
+				<option value="-l y">log on the y-axis</option>
+				<option value="-l xy">log on the x- and y-axis</option>
+		</param>
 		
 		<param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
 		<param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
@@ -117,7 +118,7 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/>
+		<data name="outputFilePNG" format="png" label="[plot transcript list] output file"/>
 	</outputs> 
 	
 	<help>