--- a/plotHeatmap.xml	Fri May 13 14:03:24 2016 -0400
+++ b/plotHeatmap.xml	Mon Sep 19 17:49:56 2016 -0400
@@ -21,6 +21,10 @@
                 #if $outFileSortedRegions:
                     --outFileSortedRegions "$outFileSortedRegions"
                 #end if
+
+                #if $output.dpi:
+                    --dpi "$output.dpi"
+                #end if
             #else
                 --plotFileFormat 'png'
             #end if
@@ -42,12 +46,18 @@
                     --missingDataColor '$advancedOpt.missingDataColor'
                 #end if
 
-                --colorMap '$advancedOpt.colorMap'
+                #if str($advancedOpt.colorMap).strip() != "":
+                    --colorMap #echo " ".join(str($advancedOpt.colorMap).strip().split(","))#
+                #end if
+                --alpha '$advancedOpt.alpha'
+                #if str($advancedOpt.colorList).strip() != "":
+                    --colorList $advancedOpt.colorList
+                #end if
 
                 #if str($advancedOpt.zMin).strip() != "":
                     --zMin $advancedOpt.zMin
                 #end if
-                #if $advancedOpt.zMax:
+                #if str($advancedOpt.zMax).strip() != "":
                     --zMax $advancedOpt.zMax
                 #end if
 
@@ -91,10 +101,12 @@
 ]]>
     </command>
     <inputs>
-        <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/>
+        <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+               label="Matrix file from the computeMatrix tool" help=""/>
 
         <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
+            <expand macro="output_dpi" />
             <expand macro="input_save_matrix_values" />
         </expand>
 
@@ -125,11 +137,18 @@
                     Alternatively colors can be specified using the #rrggbb notation." />
 
                 <expand macro="colorMap" />
+                <param argument="--alpha" type="float" value="1.0" min="0.0"
+                    max="1.0" optional="True"
+                    label="Alpha channel (transparency)"
+                    help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
+                    be between 0 and 1. A value of 0.0 would be fully transparent." />
 
-                <param argument="--zMin" type="float" value="" size="3" optional="True"
-                    label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/>
-                <param argument="--zMax" type="float" value="" size="3" optional="True"
-                    label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/>
+                <param argument="--colorList" type="text" value="" size="50" optional="True"
+                    label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
+                    help="The color of the heatmaps can be specified as a list of colors separated by comas with
+                    not space in between. For example: white,blue white,green will set a color map from white
+                    to blue for the first heatmap and for white to green for the next heatmap."/>
+                <expand macro="zMin_zMax" />
                 <param argument="--yMin" type="float" value="" size="3" optional="True"
                     label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
                 <param argument="--yMax" type="float" value="" size="3" optional="True"