--- a/scHicAdjustMatrix.xml	Thu Jan 23 20:55:14 2020 +0000
+++ b/scHicAdjustMatrix.xml	Tue Mar 10 18:59:09 2020 +0000
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
         --action $action_selector
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
@@ -16,7 +16,7 @@
         #end if
 
 
-        --outFileName adjusted_matrix.mcool
+        --outFileName adjusted_matrix.scool
 
         --threads @THREADS@
 
@@ -25,7 +25,7 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="action_selector" type="select" label="Action to take apply on matrices:">
                 <option value="keep" selected="True">Keep the listed chromosomes</option>
                 <option value="remove" >Remove the listed chromosomes</option>
@@ -33,14 +33,14 @@
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="adjusted_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: merged matrix"/>
+        <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='keep' />
             <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' />
-            <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, 
@@ -201,7 +201,7 @@
 Adjust all matrices
 ===================
 
-scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the mcool file.
+scHicAdjustMatrix is a tool to keep or remove a list of chromosomes of all Hi-C matrices stored in the scool file.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_