# HG changeset patch
# User iuc
# Date 1753980663 0
# Node ID 3728380d1dff00cf1b9a616c8f879fb81aa4c7ae
# Parent  baa3ae7ac42cc2c5926cef2acb982c55f512fd7c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b

diff -r baa3ae7ac42c -r 3728380d1dff macros.xml
--- a/macros.xml	Fri Apr 14 14:29:00 2023 +0000
+++ b/macros.xml	Thu Jul 31 16:51:03 2025 +0000
@@ -3,6 +3,12 @@
     <token name="@TOOL_VERSION@">4</token>
     <token name="@PROFILE@">22.05</token>
 
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">hicexplorer</xref>
+        </xrefs>
+    </xml>
+
      <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement>
@@ -173,4 +179,4 @@
             <option value="plasma_r">plasma reversed</option>
         </param>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r baa3ae7ac42c -r 3728380d1dff scHicCluster.xml
--- a/scHicCluster.xml	Fri Apr 14 14:29:00 2023 +0000
+++ b/scHicCluster.xml	Thu Jul 31 16:51:03 2025 +0000
@@ -4,6 +4,7 @@
         <token name="@BINARY@">scHicCluster</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
@@ -29,7 +30,7 @@
 
     ]]></command>
     <inputs>
-        
+
         <expand macro="matrix_scooler_macro"/>
         <param name="clusterMethod_selector" type="select" label="Cluster method:">
                 <option value="kmeans" selected="True">K-means</option>
@@ -40,8 +41,8 @@
                 <option value="knn" >Exact k-nearest neighbors</option>
                 <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="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>
@@ -85,9 +86,9 @@
 Clustering on raw data
 ======================
 
-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 such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. 
+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 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_