--- a/chicViewpointBackgroundModel.xml	Fri Dec 11 21:33:57 2020 +0000
+++ b/chicViewpointBackgroundModel.xml	Tue Mar 16 15:17:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>compute a background model for cHi-C / HiChIP data</description>
     <macros>
         <token name="@BINARY@">chicViewpointBackgroundModel</token>
@@ -13,7 +13,6 @@
         #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
 
         @BINARY@
-
             --matrices $m
             --averageContactBin $averageContactBin
             --fixateRange $fixateRange
@@ -21,32 +20,42 @@
             $truncateZeros
             --threads @THREADS@
             --outFileName background.txt
-    ]]></command>
+    ]]>    </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 name='truncateZeros' type='boolean' truevalue='--truncateZeros'  falsevalue="" checked="false" label="Truncate zeros"
-                    help="Set this parameter if you want truncate zeros to fight over dispersion."/>
+        <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='--truncateZeros' type='boolean' truevalue='--truncateZeros' falsevalue="" checked="false" label="Truncate zeros" help="Set this parameter if you want truncate zeros to fight over dispersion." />
     </inputs>
     <outputs>
-        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
+        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model" />
     </outputs>
     <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.txt" ftype="tabular" compare="sim_size" delta='40000'/>
+        <test expect_num_outputs="1">
+            <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" ftype="tabular">
+                <assert_contents>
+                    <has_text text="-500000" />
+                    <has_text text="-498000" />
+                    <has_n_columns n="5" />
+                    <has_text text="nbinom" />
+                </assert_contents>
+            </output>
         </test>
-        <test>
-            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
-            <param name="truncateZeros" value="True"/>
-            <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
-            <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
+        <test expect_num_outputs="1">
+            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
+            <param name="truncateZeros" value="True" />
+            <param name="referencePoints" value="cHi-C/referencePoints.bed" />
+            <output name="background" ftype="tabular">
+                <assert_contents>
+                    <has_text text="476000" />
+                    <has_text text="491000" />
+                    <has_n_columns n="5" />
+                    <has_text text="nbinom" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
@@ -63,6 +72,6 @@
 For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>