--- a/scHicCluster.xml	Thu Jan 23 15:57:55 2020 -0500
+++ b/scHicCluster.xml	Tue Mar 10 15:06:22 2020 -0400
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
 
         --numberOfClusters $numberOfClusters
 
@@ -20,7 +20,7 @@
         #end if
 
         --dimensionReductionMethod $dimensionReductionMethod_selector
-
+        --numberOfNearestNeighbors $numberOfNearestNeighbors
         --outFileName cluster_list.txt
 
         --threads @THREADS@
@@ -30,7 +30,7 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name="clusterMethod_selector" type="select" label="Cluster method:">
                 <option value="kmeans" selected="True">K-means</option>
                 <option value="spectral" >Spectral clustering</option>
@@ -41,6 +41,7 @@
                 <option value="pca" >Principal components</option>
         </param>
         <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />   
+        <param name="numberOfNearestNeighbors" type="integer" value="100"  label="Number of nearest neighbors" help='How many nearest neighbors should be computed for the k-nn graph?' />   
 
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
@@ -49,14 +50,14 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='dimensionReductionMethod_selector' value='none' />
             <param name='numberOfClusters' value='7' />
             <output name="outFileName" file="scHicCluster/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='kmeans' />
             <param name='dimensionReductionMethod_selector' value='none' />
             <param name='numberOfClusters' value='7' />
@@ -65,14 +66,14 @@
             <output name="outFileName" file="scHicCluster/cluster_kmeans_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='spectral' />
             <param name='dimensionReductionMethod_selector' value='knn' />
             <param name='numberOfClusters' value='7' />
             <output name="outFileName" file="scHicCluster/cluster_spectral_knn.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusterMethod_selector' value='spectral' />
             <param name='dimensionReductionMethod_selector' value='pca' />
             <param name='numberOfClusters' value='7' />
@@ -86,8 +87,8 @@
 
 scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
 The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. 
-Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 
-can be faster or less memory demanding.
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. 
+They can give you better results, can be faster or less memory demanding.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_