--- a/bamCoverage.xml	Mon Dec 16 15:13:08 2013 -0500
+++ b/bamCoverage.xml	Sat Dec 21 14:26:06 2013 -0500
@@ -26,10 +26,6 @@
             --scaleFactor $scaling.scaleFactor
         #end if
 
-        ##if str($ignoreForNormalization).strip() != '':
-        ##  --ignoreForNormalization $ignoreForNormalization
-        ##end if
-
         #if $advancedOpt.showAdvancedOpt == "yes":
             #if $advancedOpt.smoothLength:
                 --smoothLength '$advancedOpt.smoothLength'
@@ -45,6 +41,10 @@
                 --minMappingQuality '$advancedOpt.minMappingQuality'
             #end if
 
+            ##if str($advancedOpt.ignoreForNormalization).strip() != '':
+            ##    --ignoreForNormalization $advancedOpt.ignoreForNormalization
+            ##end if
+
         #end if
     </command>
 
@@ -80,13 +80,6 @@
             </when>
         </conditional>
 
-    <!--
-    Not yet supported.
-    <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" />
-    -->
-
         <param name="outFileFormat" type="select" label="Coverage file format">
             <option value="bigwig" selected="true">bigwig</option>
             <option value="bedgraph">bedgraph</option>
@@ -118,6 +111,11 @@
                 <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. *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="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>
     </inputs>