--- a/bamCompare.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamCompare.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,12 +1,16 @@
 <tool id="bamCompare" name="bamCompare" version="1.0">
   <description>Normalize and compare two BAM files to output ratio, log2ratio or difference.</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="1.7.1">numpy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
   </requirements>
   <command>
   bamCompare
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bamfile1 '$bamFile1'
   -bai1 '${bamFile1.metadata.bam_index}'
   --bamfile2 '$bamFile2'
@@ -28,8 +32,7 @@
   #end if
 
   --ratio $comparison.type
-  
-  
+
   #if $comparison.type=='subtract':
     #if $comparison.normalization.type=='rpkm':
       --normalizeUsingRPKM
@@ -37,27 +40,26 @@
       --normalizeTo1x $comparison.normalization.normalizeTo1x
     #end if
   #end if
-  
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if $advancedOpt.smoothLength:
       --smoothLength '$advancedOpt.smoothLength'
     #end if
-    
+
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
     #end if
+
     $advancedOpt.doNotExtendPairedEnds
     $advancedOpt.ignoreDuplicates
-    
+
     #if $advancedOpt.minMappingQuality:
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
-    
+
     --missingDataAsZero $advancedOpt.missingDataAsZero
-    
+
   #end if
-  --numberOfProcessors 4
-  
 
   </command>
 
@@ -76,7 +78,6 @@
        label="Bin size in bp"
        help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
 
-
     <conditional name="scaling">
       <param name="method" type="select" 
          label="Method to use for scaling the largest sample to the smallest">
@@ -130,41 +131,40 @@
         <option value="bigwig" selected="true">bigwig</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="smoothLength" type="integer" value="1" optional="true" min="1"
-       label="Smooth values using the following length (in bp)"
-       help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+
+    <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="smoothLength" type="integer" value="1" optional="true" min="1"
+            label="Smooth values using the following length (in bp)"
+            help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+
+        <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="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="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
-        label="Do not extend paired ends"
-        help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
-      
-     <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
-        label="Ignore duplicates"
-        help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
-      
-      <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
-        label="Minimum mapping quality"
-        help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
-        
-      <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." />
+        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
+            label="Do not extend paired ends"
+            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
+
+        <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
+            label="Ignore duplicates"
+            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
 
-    </when>
- </conditional>
+        <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
+            label="Minimum mapping quality"
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
+
+        <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." />
+        </when>
+    </conditional>
 
   </inputs>
   <outputs>