--- a/deepTools_macros.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/deepTools_macros.xml	Mon May 25 05:16:10 2015 -0400
@@ -13,23 +13,53 @@
                 <expand macro="doNotExtendPairedEnds" />
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
-                <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
-                    label="Include zeros"
-                    help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
-                <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
-                    help="If not specified the value is set automatically. (--zMin)"/>
-                <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
-                    help="If not specified the value is set automatically. (--zMax)"/>
+                <expand macro="includeZeros" />
+                <expand macro="zMin_zMax" />
                 <expand macro="colormap" />
             </when>
         </conditional>
     </xml>
 
+
+    <xml name="bigwigCorrelate_mode_actions">
+
+        <expand macro="region_limit_operation" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <expand macro="includeZeros" />
+                <expand macro="zMin_zMax" />
+                <expand macro="colormap" />
+                <expand macro="plotTitle" />
+                <expand macro="plotNumbers" />
+            </when>
+        </conditional>
+    </xml>
+
+
+    <xml name="includeZeros">
+        <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
+            label="Include zeros"
+            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
+    </xml>
+    <xml name="zMin_zMax">
+        <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMin)"/>
+        <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMax)"/>
+    </xml>
+
     <xml name="region_limit_operation">
         <param name="region" type="text" value=""
             label="Region of the genome to limit the operation to"
             help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;. (--region)" />
     </xml>
+
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
     <token name="@WRAPPER_VERSION@">1.5.9.2</token>
     <xml name="requirements">
@@ -39,6 +69,7 @@
             <requirement type="package" version="1.5.9">deepTools</requirement>
             <yield />
         </requirements>
+        <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
     </xml>
 
@@ -77,6 +108,16 @@
         #end if
     </token>
 
+    <xml name="samFlag">
+        <param name="samFlag" type="integer" optional="true" value=""
+            label="Filter reads based on the SAM flag"
+            help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
+    </xml>
+    <xml name="plotNumbers">
+        <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
+            label="Plot the correlation value" 
+            help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
+    </xml>
     <xml name="doNotExtendPairedEnds">
         <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
             label="Do not extend paired ends"
@@ -141,11 +182,6 @@
 .. _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>
@@ -162,7 +198,24 @@
             <param name="label" type="text" size="30" optional="true" value=""
                 label="Label"
                 help="Label to use in the output. If not given the dataset name will be used instead."/>
-          </repeat>
+        </repeat>
+    </xml>
+
+    <xml name="multiple_input_bigwigs">
+        <repeat name="input_files" title="BigWig files" min="2">
+            <param name="bigwigfile" type="data" format="bigwig" 
+                label="Bigwig file" 
+                help="The Bigwig file must be sorted."/>
+            <param name="label" type="text" size="30" optional="true" value=""
+                label="Label"
+                help="Label to use in the output. If not given the dataset name will be used instead."/>
+        </repeat>
+    </xml>
+
+    <xml name="plotTitle">
+        <param name="plotTitle" type="text" value="" size="30" optional="True"
+            label="Title of the plot"
+            help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
     </xml>
 
     <token name="@multiple_input_bams@">
@@ -187,6 +240,27 @@
         #end for
     </token>
 
+    <token name="@multiple_input_bigwigs@">
+        #import tempfile
+        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+        #set files=[]
+        #set labels=[]
+        #for $i in $input_files:
+            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+            #set $temp_input_path = $temp_input_handle.name
+            #silent $temp_input_handle.close()
+            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
+            #silent $files.append('%s.bw' % $temp_input_path)
+
+            ##set $files += [str($i.bigwigfile)]
+            #if str($i.label.value) != "":
+                #set $labels += ["\"%s\"" % ($i.label.value)]
+            #else
+                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
+            #end if
+        #end for
+    </token>
+
     <xml name="reference_genome_source">
         <conditional name="source">
             <param name="ref_source" type="select" label="Reference genome">