--- a/hicBuildMatrix.xml	Sat Jun 09 15:00:27 2018 -0400
+++ b/hicBuildMatrix.xml	Mon Dec 09 10:27:01 2019 +0000
@@ -5,13 +5,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" >
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 
         mkdir ./QCfolder &&
         mkdir $qc.files_path &&
-        hicBuildMatrix
+        @BINARY@
 
             --samFiles
             #for $repeat in $samFiles:
@@ -25,7 +25,10 @@
             #end if
 
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
-                --binSize $restrictionCutFileBinSize_conditional.binSize
+                --binSize 
+                #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
+                    '${repeat.binSize}'
+                #end for
             #end if
 
 
@@ -63,7 +66,7 @@
         && mv $qc.files_path/*.log raw_qc
         && mv matrix.$outputFormat matrix
         #if $outBam_Boolean:
-            && samtools sort ./unsorted.bam -o sorted.bam
+            && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
         #end if
 
 ]]>
@@ -93,9 +96,10 @@
                               is too far away from the nearest restriction site." />
             </when>
             <when value="optionBinSize">
-                <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. "/>
+                <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>
             </when>
         </conditional>
 
@@ -158,12 +162,41 @@
             </repeat>
             <conditional name="restrictionCutFileBinSize_conditional">
                 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <param name="binSize" value="5000"/>
+                <repeat name='binSizes'>
+                    <param name="binSize" value="5000"/>
+                </repeat>
             </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" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
+            <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="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
         </test>
     </tests>