--- a/bamCompare.xml	Fri May 13 17:39:53 2016 -0400
+++ b/bamCompare.xml	Thu Aug 11 06:32:21 2016 -0400
@@ -65,6 +65,8 @@
                 #if str($advancedOpt.ignoreForNormalization).strip() != '':
                     --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
                 #end if
+
+                @blacklist@
             #end if
 ]]>
     </command>
@@ -105,12 +107,16 @@
                 label="How to compare the two files"
                 help="The default is to output the log2ratio between the two samples.
                 The reciprocal ratio returns the negative of the inverse of the ratio if
-                the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
+                the ratio is less than 0. The resulting values are interpreted as negative
+                fold changes. To output the scaled values from the first or second BAM file,
+                select 'first' or 'second'.">
                 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
                 <option value="ratio">Compute the ratio of the number of reads</option>
                 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
                 <option value="add">Compute the sum of number of reads</option>
                 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
+                <option value="first">Returns the scaled value of the first BAM file</option>
+                <option value="second">Returns the scaled value of the second BAM file</option>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />
@@ -119,6 +125,8 @@
                 <expand macro="pseudocount" />
             </when>
             <when value="add" />
+            <when value="first" />
+            <when value="second" />
             <when value="reciprocal_ratio">
                 <expand macro="pseudocount" />
             </when>
@@ -154,12 +162,14 @@
                 <expand macro="read_processing_options" />
 
                 <expand macro="skipNAs" />
+
                 <param argument="--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 of copy number variations between samples then you may want to exclude these.
                         Another typical example is the difference in chromosome X copies between males and females in many species.
                         Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
+                <expand macro="blacklist" />
             </when>
         </conditional>
     </inputs>