--- a/multiBamSummary.xml	Wed Aug 22 16:26:35 2018 -0400
+++ b/multiBamSummary.xml	Tue Feb 19 09:56:34 2019 -0500
@@ -23,6 +23,10 @@
                 --outRawCounts '$outFileRawCounts'
             #end if
 
+            #if $scalingFactors:
+                --scalingFactors '$scalingFactorsFile'
+            #end if
+
             #if $mode.modeOpt == "bins":
                 --binSize '$mode.binSize'
                 --distanceBetweenBins '$mode.distanceBetweenBins'
@@ -44,6 +48,7 @@
 
     <inputs>
         <expand macro="multiple_input_bams" MIN="2"/>
+        <expand macro="custom_sample_labels" />
 
         <conditional name="mode">
             <param name="modeOpt" type="select" label="Choose computation mode"
@@ -79,6 +84,7 @@
         </expand>
 
         <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
+        <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/>
 
     </inputs>
     <outputs>
@@ -86,6 +92,9 @@
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>outRawCounts is True</filter>
         </data>
+        <data format="tabular" name="scalingFactorsFile" label="${tool.name} on ${on_string}: scaling factors">
+            <filter>scalingFactors is True</filter>
+        </data>
     </outputs>
     <tests>
         <test>