--- a/hicBuildMatrix.xml	Sat Dec 16 16:26:37 2017 -0500
+++ b/hicBuildMatrix.xml	Sat Dec 30 08:21:48 2017 -0500
@@ -21,7 +21,7 @@
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
                 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
                 --minDistance $restrictionCutFileBinSize_conditional.minDistance
-                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize          
+                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
             #end if
 
             #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
@@ -37,7 +37,11 @@
                 --region '$region'
             #end if
 
-            --outFileName ./matrix.h5
+            #if $outputFormat == 'h5'
+                --outFileName matrix.h5
+            #elif $outputFormat == 'cool'
+                --outFileName matrix.cool
+            #end if
             --outBam ./unsorted.bam
 
             $keepSelfCircles
@@ -110,26 +114,37 @@
                     and that are considered un-ligated fragments or 
                     'dangling-ends'. If not given, such statistics will 
                     not be available."/>
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='h5'>HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
     </inputs>
     <outputs>
         <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
-        <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
+        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
         <data name="qc" format="html" label="${tool.name} QC"/>
     </outputs>
     <tests>
         <test>
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
+                <param name="samFile" value="small_test_R1_unsorted.sam"/>
             </repeat>
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
+                <param name="samFile" value="small_test_R2_unsorted.sam"/>
             </repeat>
             <conditional name="restrictionCutFileBinSize_conditional">
                 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
                 <param name="binSize" value="5000"/>
             </conditional>
+            <param name='outputFormat' value='h5'/>
+
             <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
-            <output name="outFileName" file="small_test_matrix.h5" ftype="h5" compare="sim_size" delta="30000"/>
+            <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -138,8 +153,8 @@
 ===============================
 
 ``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files 
-corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
- not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 
+corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should 
+not be sorted by position. There are two main options to create the Hi-C contact matrix, either by 
 fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length. 
 ``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.
 
@@ -201,6 +216,7 @@
 .. image:: $PATH_TO_IMAGES/hicQC.png
    :width: 70 %
 
+
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html