--- a/bigwigCompare.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bigwigCompare.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,12 +1,16 @@
 <tool id="bigwigCompare" name="bigwigCompare" version="1.0">
   <description>compares two bigwig files based on the number of mapped reads</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
   <command>
   bigwigCompare
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bigwig1 '$bigwigFile1'
   --bigwig2 '$bigwigFile2'
 
@@ -14,26 +18,22 @@
   --outFileFormat '$outFileFormat'
 
   --ratio $comparison_type
-  
-  #if $advancedOpt.showAdvancedOpt == "yes":
-    #if str($advancedOpt.region.value) != '':
-      --region '$advancedOpt.region'
+
+    #if $advancedOpt.showAdvancedOpt == "yes":
+      #if str($advancedOpt.region.value) != '':
+        --region '$advancedOpt.region'
+      #end if
+
+      --missingDataAsZero $advancedOpt.missingDataAsZero
+      --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+      --pseudocount '$advancedOpt.pseudocount'
+      --binSize $advancedOpt.binSize
+
     #end if
-  
-    --missingDataAsZero $advancedOpt.missingDataAsZero
-    --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
-    --pseudocount '$advancedOpt.pseudocount'
-    --binSize $advancedOpt.binSize
-    
-  #end if
-  --numberOfProcessors 4
-  
 
   </command>
-
   <inputs>
     <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
-
     <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
 
       <param name="comparison_type" type="select" 
@@ -48,36 +48,33 @@
 
     <param name="outFileFormat" type="select" label="Coverage file format">
         <option value="bigwig" selected="true">bigwig</option>
-    <option value="bedgraph">bedgraph</option>
+        <option value="bedgraph">bedgraph</option>
     </param>
-    
-        <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">
-      
-          <param name="binSize" type="integer" value="50" min="1" 
-       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." />
-    
-    <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
-    <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
-    <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+
+    <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">
+            <param name="binSize" type="integer" value="50" min="1" 
+                label="Bin size in bp"
+                help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
 
-    </when>
- </conditional>
+            <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." />
+
+            <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
+            <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
+            <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+        </when>
+    </conditional>
   </inputs>
   <outputs>
     <data format="bigwig" name="outFileName">