--- a/scHicPlotClusterProfiles.xml	Thu Jan 23 20:54:33 2020 +0000
+++ b/scHicPlotClusterProfiles.xml	Tue Mar 10 18:58:05 2020 +0000
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix $matrix_mcooler
+        --matrix $matrix_scooler
         --clusters $clusters
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
@@ -33,7 +33,7 @@
 
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
         <param name="maximalDistance" type="integer" value="2000000"  label="Maximal distance" help='Maximal distance to consider for plotting' />   
         <conditional name="order_by_conditional">
@@ -59,7 +59,7 @@
         
     </inputs>
     <outputs>
-        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
@@ -68,7 +68,7 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' />
             <conditional name="order_by_conditional">
                 <param name="order_by_selection" value="svl"/>
@@ -88,7 +88,8 @@
 Plot cluster profiles
 =====================
 
-scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix assoziated to a cluster, within the cluster the matrices can be order either via their short vs long range ratio or by the order of the file.
+scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix associated to a cluster, within the cluster the matrices can be ordered either via their short vs long range ratio or by the order of the file.
+This tool is useful as a quality control of a cluster to check if all matrices assigned to that cluster are displaying similar contacts distribution.
 
 .. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png
    :width: 50%