--- a/computeMatrix.xml	Tue Sep 17 10:27:29 2013 -0400
+++ b/computeMatrix.xml	Tue Oct 29 17:26:28 2013 -0400
@@ -1,11 +1,11 @@
 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
-  <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>
-  <requirements>
-    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
-    <requirement type="package" >deepTools</requirement>
-  </requirements>
-  <command>
-    #import tempfile
+    <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" />
+    <macros>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <command>
+        #import tempfile
 
     #set $temp_input_handle = tempfile.NamedTemporaryFile()
     #set $temp_input_path = $temp_input_handle.name
@@ -28,7 +28,7 @@
   --scoreFileName '$scoreFile'
   --outFileName '$outFileName'
 
-  --numberOfProcessors 4
+    @THREADS@
 
   #if $output.showOutputSettings == "yes"
       #if $output.saveData:
@@ -208,19 +208,28 @@
         </test>
     </tests>
   <help>
+
 **What it does**
 
-This tool summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile. Typically, these genomic regions are genes, but any other regions defined in a BED or INTERVAL format can be used. This tool can also be used to filter and sort regions according to their score.
+This tool summarizes and prepares an intermediary file
+containing scores associated with genomic regions that can be used
+afterwards to plot a heatmap or a profile.
+
+Genomic regions can really be anything - genes, parts of genes, ChIP-seq
+peaks, favorite genome regions... as long as you provide a proper file
+in BED or INTERVAL format. This tool can also be used to filter and sort
+regions according to their score.
+
+
+.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
+   :alt: Relationship between computeMatrix, heatmapper and profiler
+
 
 -----
 
 .. class:: infomark
 
-If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
-
-This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
+@REFERENCES@
 
-.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
-.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-  </help>
+    </help>
 </tool>