--- a/genetrack.xml	Wed Dec 02 16:15:05 2015 -0500
+++ b/genetrack.xml	Wed Dec 16 12:22:27 2015 -0500
@@ -38,8 +38,8 @@
         </conditional>
         <param name="sigma" type="integer" value="5" min="1" label="Sigma to use when smoothing reads" help="Higher values increase computation but produce more smoothing." />
         <param name="exclusion" type="integer" value="20" min="1" label="Peak exclusion zone" help="Exclusion zone around each peak that prevents others from being called." />
-        <param name="up_width" type="integer" value="10" min="0" label="Upstream width of called peaks" />
-        <param name="down_width" type="integer" value="10" min="0" label="Downstream width of called peaks" />
+        <param name="up_width" type="integer" value="10" min="0" label="Exclusion zone of upstream called peaks" />
+        <param name="down_width" type="integer" value="10" min="0" label="Exclusion zone of downstream called peaks" />
         <param name="filter" type="integer" value="3" min="0" label="Absolute read filter" help="Removes peaks with lower peak height." />
     </inputs>
     <outputs>
@@ -88,22 +88,32 @@
     <help>
 **What it does**
 
-Genetrack supports ChIP experiments.  The peak caller takes a standard set of data on both the sense and
-antisense strands (ScIdx format) and smooths their relative reads. It then predicts the peaks present in
-the smoothed dataset and uses those peak locations to find the maximal non-overlapping subset.  It then
-selects the highest peak and establishes an exclusion zone, and no other predicted peaks will be reported
-within the exclusion zone.  Finally, it ensures each peak is above a threshold and that two peaks are not
-too close to each other.
+<![CDATA[
+
+GeneTrack separately identifies peaks on the forward "+” and reverse “-” strand.  The way that GeneTrack works
+is to replace each tag with a probabilistic distribution of occurrences for that tag at and around its mapped
+genomic coordinate.  The distance decay of the probabilistic distribution is set by adjusting the value of the
+tool's **Sigma to use when smoothing reads** parameter.  GeneTrack then sums the distribution over all mapped
+tags.  This results in a smooth continuous trace that can be globally broadened or tightened by adjusting the
+sigma value.  GeneTrack starts with the highest smoothed peak first, treating each strand separately if indicated
+by the data, then sets up an exclusion zone (centered over the peak) defined by the value of the **Peak exclusion
+zone** parameter (see figure).  The exclusion zone prevents any secondary peaks from being called on the same strand
+within that exclusion zone.  In rare cases, it may be desirable to set different exclusion zones upstream (more 5’)
+versus downstream (more 3’) of the peak.
+
+]]>
+
+.. image:: $PATH_TO_IMAGES/genetrack.png
 
 -----
 
 **Options**
 
-* **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
-* **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
-* **Upstream width of called peaks** - Upstream width of called peaks.
-* **Downstream width of called peaks** - Downstream width of called peaks.
-* **Filter** - Absolute read filter.  Restricts output to only peaks with larger peak height.
+* **Sigma to use when smoothing reads** - Smooths clusters of tags via a Gaussian distribution.
+* **Peak exclusion zone** - Exclusion zone around each peak, eliminating all other peaks on the same strand that are within a ± bp distance of the peak.
+* **Exclusion zone of upstream called peaks** - Defines the exclusion zone centered over peaks upstream of a peak.
+* **Exclusion zone of downstream called peaks** - Defines the exclusion zone centered over peaks downstream of a peak.
+* **Filter** - Absolute read filter, restricts output to only peaks with larger peak height.
     </help>
     <expand macro="citations" />
 </tool>