--- a/bigwigCompare.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/bigwigCompare.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.2">
+<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.3">
     <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bigwigCompare</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -18,10 +19,11 @@
 
         --ratio $comparison_type
 
+        #if str(region).strip() != '':
+            --region 'region'
+        #end if
+
         #if $advancedOpt.showAdvancedOpt == "yes":
-          #if str($advancedOpt.region.value) != '':
-            --region '$advancedOpt.region'
-          #end if
 
           --missingDataAsZero $advancedOpt.missingDataAsZero
           --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
@@ -49,6 +51,8 @@
             <option value="bedgraph">bedgraph</option>
         </param>
 
+        <expand macro="region_limit_operation" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -60,10 +64,6 @@
                     label="Bin size in bp"
                     help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
 
-                <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;" />
-
                 <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 replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
@@ -93,10 +93,9 @@
 finally a summarizing value is reported. This value can be the ratio of the
 number of reads per bin, the log2 of the ratio, the sum or the difference.
 
+
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>