--- a/bamCompare.xml	Tue Aug 06 08:20:47 2013 -0400
+++ b/bamCompare.xml	Wed Aug 14 07:18:18 2013 -0400
@@ -1,9 +1,10 @@
-<tool id="bamCompare" name="bamCompare" version="1.0">
+<tool id="deeptools_bamCompare" name="bamCompare" version="1.0">
   <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference.</description>
   <requirements>
-    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
+    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
+    <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
   bamCompare
@@ -34,11 +35,16 @@
   --ratio $comparison.type
 
   #if $comparison.type=='subtract':
-    #if $comparison.normalization.type=='rpkm':
-      --normalizeUsingRPKM
-    #elif $comparison.normalization.type=='1x':
-      --normalizeTo1x $comparison.normalization.normalizeTo1x
-    #end if
+      #if $comparison.normalization.type=='rpkm':
+        --normalizeUsingRPKM
+      #elif $comparison.normalization.type=='1x':
+        --normalizeTo1x $comparison.normalization.normalizeTo1x
+      #end if
+
+      #if str($comparison.ignoreForNormalization).strip() != '':
+        --ignoreForNormalization $comparison.ignoreForNormalization
+      #end if
+
   #end if
 
   #if $advancedOpt.showAdvancedOpt == "yes":
@@ -65,10 +71,10 @@
 
   <inputs>
     <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
-       help="The BAM file must be sorted and indexed."/>
+       help="The BAM file must be sorted."/>
 
     <param name="bamFile2" format="bam" type="data" label="Input BAM file"
-       help="The BAM file must be sorted and indexed."/>
+       help="The BAM file must be sorted."/>
 
     <param name="fragmentLength" type="integer" value="300" min="1"
        label="Length of the average fragment size"
@@ -124,6 +130,9 @@
                help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
           </when>
         </conditional>
+        <param name="ignoreForNormalization" type="text" value="" size="50"
+            label="regions that should be excluded for calculating the scaling factor"
+            help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
       </when>
     </conditional>
 
@@ -158,7 +167,7 @@
 
         <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
             label="Minimum mapping quality (e.g. BOWTIE2 measures)"
-            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
 
         <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
             label ="Treat missing data as zero"
@@ -194,7 +203,7 @@
 
 .. class:: infomark
 
-If you would like to give us feedback or you run into any trouble, please sent an email to deeptools@googlegroups.com
+If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.