--- a/hicBuildMatrix.xml	Mon Dec 09 10:27:01 2019 +0000
+++ b/hicBuildMatrix.xml	Mon Dec 16 13:19:21 2019 +0000
@@ -11,7 +11,7 @@
 
         mkdir ./QCfolder &&
         mkdir $qc.files_path &&
-        @BINARY@
+        hicBuildMatrix
 
             --samFiles
             #for $repeat in $samFiles:
@@ -25,10 +25,7 @@
             #end if
 
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
-                --binSize 
-                #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
-                    '${repeat.binSize}'
-                #end for
+                --binSize $restrictionCutFileBinSize_conditional.binSize
             #end if
 
 
@@ -96,10 +93,9 @@
                               is too far away from the nearest restriction site." />
             </when>
             <when value="optionBinSize">
-                <repeat  name='binSizes' title='Bin size in bp' min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
-                        Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
-                    <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/>
-                </repeat>
+                <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
+                    help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
+                    Otherwise all reads in the interval are considered. "/>
             </when>
         </conditional>
 
@@ -162,41 +158,12 @@
             </repeat>
             <conditional name="restrictionCutFileBinSize_conditional">
                 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <repeat name='binSizes'>
-                    <param name="binSize" value="5000"/>
-                </repeat>
+                <param name="binSize" value="5000"/>
             </conditional>
             <param name='outputFormat' value='h5'/>
             <param name='outBam_Boolean' value="True" />
             <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
-            <output name="outFileName" ftype="h5">
-                <assert_contents>
-                    <has_h5_keys keys='intervals,matrix'/>
-                </assert_contents>
-            </output>
-            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
-        </test>
-         <test>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam"/>
-            </repeat>
-            <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam"/>
-            </repeat>
-            <conditional name="restrictionCutFileBinSize_conditional">
-                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <repeat name='binSizes'>
-                    <param name="binSize" value="5000"/>
-                </repeat>
-            </conditional>
-            <param name='outputFormat' value='cool'/>
-            <param name='outBam_Boolean' value="True" />
-            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
-            <output name="outFileName" ftype="cool">
-                <assert_contents>
-                    <has_h5_keys keys='bins,chroms,indexes,pixels'/>
-                </assert_contents>
-            </output>
+            <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size" delta="50000"/>
             <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
         </test>
     </tests>