--- a/computeMatrix.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/computeMatrix.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2">
+<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.3">
     <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -51,8 +52,8 @@
     --afterRegionStartLength $mode.afterRegionStartLength
   #else
     --regionBodyLength $mode.regionBodyLength
-    --startLabel $mode.startLabel
-    --endLabel $mode.endLabel
+    --startLabel "$mode.startLabel"
+    --endLabel "$mode.endLabel"
     #if $mode.regionStartLength.regionStartLength_select == "yes":
       --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
       --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
@@ -100,18 +101,17 @@
         <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/>
         <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
         <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-        <conditional name="regionStartLength">
-        <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
-          <option value="no" selected="true">no</option>
-          <option value="yes">yes</option>
-        </param>
-        <when value="no" />
-        <when value="yes">
-          <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
-        
-          <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
-        </when>
-        </conditional>
+            <conditional name="regionStartLength">
+                <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
+                    <option value="no" selected="true">no</option>
+                    <option value="yes">yes</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
+                    <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
+                </when>
+            </conditional>
       </when>
       
       <when value="reference-point">
@@ -208,9 +208,12 @@
    :alt: Relationship between computeMatrix, heatmapper and profiler
 
 
------
+You can find more details in the `computeMatrix wiki`_.
 
-.. class:: infomark
+.. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
+
+
+-----
 
 @REFERENCES@