--- a/plotProfiler.xml	Wed Dec 23 04:01:04 2015 -0500
+++ b/plotProfiler.xml	Wed Dec 23 07:35:12 2015 -0500
@@ -16,10 +16,6 @@
             #if $output.showOutputSettings == "yes"
                 --plotFileFormat $output.outFileFormat
 
-                #if $output.saveData:
-                    --outFileNameData "$outFileNameData"
-                #end if
-
                 #if $output.saveSortedRegions:
                     --outFileSortedRegions '$outFileSortedRegions'
                 #end if
@@ -49,7 +45,7 @@
                     --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )#
                 #end if
 
-                $advancedOpt.onePlotPerGroup
+                $advancedOpt.perGroup
 
                 #if $advancedOpt.yMin:
                     --yMin $advancedOpt.yMin
@@ -124,7 +120,7 @@
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-                <param argument="--regionsLabel" type="text" value="genes" size="30"
+                <param argument="--regionsLabel" type="text" value="coverage" size="30"
                     label="Labels for the regions plotted in the heatmap"
                     help="If more than one region is being plotted a list of labels separated
                     by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
@@ -138,11 +134,12 @@
                         message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
                 </param>
 
-                <param argument="--onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
+                <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
                     label="Do one plot per group"
-                    help="When the region file contains groups separated by &quot;#&quot;, the default is
-                    to plot the averages for the distinct plots in one plot. If this option is set, each group
-                    will get its own plot, stacked on top of each other." />
+                    help="When clustering is applied to the data, or the region file contains groups separated by &quot;#&quot;,
+                    plot the groups next to each other. The default is to plot the samples next to each other.
+                    If this option is set, each group (or cluster) will get its own plot, with different samples
+                    stacked on top of each other." />
 
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
@@ -188,7 +185,7 @@
    :alt: Meta-gene profile of Rna Polymerase II
 
 
-You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler
+You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotProfile.html
 
 
 -----