--- a/chicViewpointBackgroundModel.xml	Wed Feb 05 19:48:12 2020 -0500
+++ b/chicViewpointBackgroundModel.xml	Wed Mar 11 17:18:30 2020 -0400
@@ -6,12 +6,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-   
+
         #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
             ln -s '$m' '${counter}_matrix.$m.ext' &&
         #end for
         #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
-       
+
         @BINARY@
 
             --matrices $m
@@ -23,13 +23,13 @@
     ]]></command>
     <inputs>
         <expand macro="matrix_h5_cooler_multiple_macro" />
-       
+
         <param argument="--referencePoints" type="data" format='interval'
                         label="Reference points"
                         help="Bed file contains all reference points which should be used to build the background model." />
-        <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>    
-        <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>    
-   
+        <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
+        <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
+
     </inputs>
     <outputs>
         <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
@@ -37,10 +37,10 @@
     <tests>
         <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
-            
+
             <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
-           
-            <output name="background" file="cHi-C/background.bed" ftype="tabular" compare="sim_size" delta='40000'/>
+
+            <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
         </test>
     </tests>
     <help><![CDATA[