--- a/SMART/galaxy/getWigDistance.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/getWigDistance.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -5,13 +5,21 @@
 	</command>
 	
     <inputs>
-    	<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."/>    
+    	<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."/>    
     </inputs>
         
     <outputs>
        	<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>