--- a/plotProfiler.xml	Mon Jan 25 20:27:28 2016 -0500
+++ b/plotProfiler.xml	Mon Feb 15 10:34:50 2016 -0500
@@ -1,6 +1,6 @@
 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
     <description>
-        creates a profile plot for a score associated to genomic regions
+        creates a profile plot for score distributions across genomic regions
     </description>
     <macros>
         <token name="@BINARY@">plotProfile</token>
@@ -35,7 +35,13 @@
                 --plotHeight $advancedOpt.plotHeight
                 --plotWidth $advancedOpt.plotWidth
                 --plotType $advancedOpt.plotType
-                --regionsLabel '$advancedOpt.regionsLabel'
+                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
+                    --samplesLabel $advancedOpt.samplesLabel
+                #end if
+
+                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
+                    --regionsLabel $advancedOpt.regionsLabel
+                #end if
 
                 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
                     --plotTitle '$advancedOpt.plotTitle'
@@ -102,9 +108,9 @@
                     label="Plot height"
                     help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
 
-                <param argument="--plotWidth" type="integer" value="8" min="1"
+                <param argument="--plotWidth" type="integer" value="11" min="1"
                     label="Plot width"
-                    help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
+                    help="Width in cm. The default value is 11 centimeters. The minimum value is 1 cm." />
 
                 <param argument="--plotType" type="select" label="Plot type"
                     help="The &quot;lines&quot; option will
@@ -120,10 +126,20 @@
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-                <param argument="--regionsLabel" type="text" value="coverage" size="30"
+                <param argument="--samplesLabel" type="text" size="30"
+                    label="Labels for the samples (each bigwig) plotted"
+                    help="The default is to use the file name of the sample. The sample labels should be separated by
+                    spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--regionsLabel" type="text" 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 commas is required. For example, &quot;label1, label2&quot;."/>
+                    help="If more than one region is being plotted a list of labels separated by space is required.
+                          If a label itself contains a space, then quotes are needed.
+                          For example, label_1, &quot;label 2&quot;" />
 
                 <expand macro="plotTitle" />
                 <param argument="--colors" type="text" value="" size="40"
@@ -135,9 +151,8 @@
                 </param>
 
                 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
-                    label="Do one plot per group"
-                    help="When clustering is applied to the data or multiple BED files were used,
-                    plot the groups next to each other. The default is to plot the samples next to each other." />
+                    label="Make one plot per group of regions"
+                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
 
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
@@ -169,21 +184,37 @@
     <help>
 <![CDATA[
 
-**What it does**
+What it does
+-------------
 
 This tool plots the average enrichments over all genomic
-regions supplied to computeMarix. It requires that computeMatrix was successfully run.
-It is a very useful complement to the heatmapper, especially in cases where you want to
-compare the scores for many different groups. Like heatmapper, profiler does not change the
-values that were compute by computeMatrix, but you can modify the color and other display properties of the plots.
+regions supplied to ``computeMarix``. It requires that ``computeMatrix`` was successfully run.
+It is a very useful complement to ``plotHeatmap``, especially in cases where you want to
+compare the scores for many different groups. Like ``plotHeatmap``, ``plotProfile`` does not change the
+values that were computed by ``computeMatrix``, but you can modify the color and other display properties of the plots.
 
+Output
+-------------
+
+.. image:: $PATH_TO_IMAGES/plotProfiler_examples.png
+   :width: 600
+   :height: 858
+
+=======
 
-.. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
-   :alt: Meta-gene profile of Rna Polymerase II
+In addition to the image, ``plotProfile`` can also generate the values underlying the profile.
+
+See the following table for the **optional output** options:
 
-
-You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html
-
++-----------------------------------+--------------------+-----------------+-----------------+
+|  **optional output type**         |  **computeMatrix** | **plotHeatmap** | **plotProfile** |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the heatmap     |  yes               | yes             | no              |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the profile     | no                 | no              | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
+| sorted and/or filtered regions    | yes                | yes             | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
 
 -----