--- a/SMART/galaxy/getWigDistance.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/getWigDistance.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,28 +1,17 @@
-<tool id="getWigDistance" name="get WIG distance">
+<tool id="getWigDistance" name="get wig distance">
     <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
     <command interpreter="python">
 		../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile
 	</command>
 	
     <inputs>
-    	<param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
-   		<param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
-		<param name="distance" type="integer" value="1000" label="Distance around positions."/>
-		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>    
+    	<param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/>
+   		<param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/>
+		<param name="distance" type="integer" value="1000" label="distance option (compulsory option)" help="Distance around position.Be Careful! The value must be upper than 0"/>
+		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>    
     </inputs>
         
     <outputs>
-       	<data name="outputFile" format="png" label="[get WIG distance] PNG output file"/>    
+       	<data name="outputFile" format="png" label="[getWigDistance] PNG output File"/>    
     </outputs> 
-
-	<help>
-Plots the average data contained in a set of WIG files (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) around the first nucleotides of a annotation file.
-
-The tool needs an transcript list, some WIG files, and a distance. For each transcript, it collects all the values around its first nucleotide, the radius being given by the distance. Then, it computes the average value for each position. A point (*x*, *y*) means that the average value in the WIG file for a nucleotide distant by *x* nucleotides from the first nucleotide of an input transcript is *y*.
-
-You can possibly use a log scale for the *y*-axis.
-	</help>
 </tool>