--- a/scHicMergeMatrixBins.xml	Thu Jan 23 16:03:51 2020 -0500
+++ b/scHicMergeMatrixBins.xml	Tue Mar 10 15:10:44 2020 -0400
@@ -8,14 +8,14 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
         --numBins $numberOfBins
        
         #if $runningWindow:
             $runningWindow
         #end if
 
-        --outFileName merged_matrices.mcool
+        --outFileName merged_matrices.scool
 
         --threads @THREADS@
 
@@ -24,19 +24,19 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="numberOfBins" type="integer" value="10"  label="Number of bins to merge" help='Number of bins to merge to achieve the desired resolution. For example: To merge a 10kb matrix to 1MB, 10kb * 100 = 1MB i.e. the value needs to be 100.' />   
         <param name='runningWindow' type='boolean' truevalue='--runningWindow' label='Running window' help='Set to merge for using a running window of length --numBins. Must be an odd number.'/>
 
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="merged_matrices.mcool" format="mcool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
+        <data name="outFileName" from_work_dir="merged_matrices.scool" format="scool" label="${tool.name} on ${on_string}: Merged matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='numberOfBins' value='10' />
-            <output name="outFileName" ftype="mcool">
+            <output name="outFileName" ftype="scool">
                 <assert_contents>
                     <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
@@ -191,11 +191,11 @@
             </output>
         </test>
        <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='numberOfBins' value='11' />
             <param name='runningWindow' value='true' />
 
-            <output name="outFileName" ftype="mcool">
+            <output name="outFileName" ftype="scool">
                 <assert_contents>
                     <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
@@ -355,8 +355,12 @@
 Change the resolution of the scHi-C matrices
 ============================================
 
-Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb bins, a matrix of 50kb bins can be derived using --numBins 10.
-
+**scHicMergeMatrixBins** is used to decrease the resolution of single cell matrices stored in a scool file by merging their adjacent bins. With this tool, you can for example create out of a 5kb
+contact matrix a 50kb one:
+Number of bins to merge = 10
+5kb * 10 = 50k
+Depending on the downstream analyses to perform on single cell Hi-C matrices generated with HiCExplorer, one might need different bin resolutions, for instance during clustering or for plotting small or large regions of consensus matrices.
+The best practice is to merge bins in uncorrected matrices, and correct the lower resolution matrices using `scHicCorrectMatrices` subsequently.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_