--- a/deepTools_macros.xml	Wed Apr 02 09:15:44 2014 -0400
+++ b/deepTools_macros.xml	Tue Sep 16 13:46:05 2014 -0400
@@ -36,7 +36,7 @@
             </when>
         </conditional>
     </xml>
-    
+
     <xml name="region_limit_operation">
         <param name="region" type="text" value=""
             label="Region of the genome to limit the operation to"
@@ -44,14 +44,14 @@
     </xml>
     
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.1</token>
+    <token name="@WRAPPER_VERSION@">1.5.9.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="binary">@BINARY@</requirement>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.8_09023018b96c23f922aa2ea553090e9df8ecf41e">deepTools</requirement>
+            <requirement type="package" version="1.5.9.1">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
@@ -109,6 +109,9 @@
             <regex match="Traceback" />
         </stdio>
     </xml>
+    <xml name="pseudocount">
+        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+    </xml>
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -119,12 +122,22 @@
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
 
-
 .. _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 site: https://github.com/fidelram/deepTools/wiki/
 
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
     </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gku365</citation>
+            <yield />
+        </citations>
+    </xml>
 
     <xml name="multiple_input_bams">
         <repeat name="input_files" title="BAM files" min="2">
@@ -219,6 +232,12 @@
         </param>
     </xml>
 
+    <xml name="missingDataAsZero">
+                <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
+                    label ="Treat missing data as zero"
+                    help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+    </xml>
+
     <xml name="input_save_matrix_values">
         <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>