# HG changeset patch
# User iuc
# Date 1753980271 0
# Node ID 38ece0c4e31654d887fc2819ef74419c4a1cafca
# Parent  33b1c99cc709712d64c87a99d7eb2ca79999e7c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b

diff -r 33b1c99cc709 -r 38ece0c4e316 macros.xml
--- a/macros.xml	Fri Apr 14 14:27:25 2023 +0000
+++ b/macros.xml	Thu Jul 31 16:44:31 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 33b1c99cc709 -r 38ece0c4e316 scHicConsensusMatrices.xml
--- a/scHicConsensusMatrices.xml	Fri Apr 14 14:27:25 2023 +0000
+++ b/scHicConsensusMatrices.xml	Thu Jul 31 16:44:31 2025 +0000
@@ -4,6 +4,7 @@
         <token name="@BINARY@">scHicConsensusMatrices</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
@@ -19,10 +20,10 @@
 
     ]]></command>
     <inputs>
-        
+
         <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'/>
-        
+
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
@@ -33,29 +34,29 @@
             <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
             <output name="outFileName" ftype="scool">
                 <assert_contents>
-                    <has_h5_keys keys='consensus_matrix_cluster_0, 
-                                        consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom, 
+                    <has_h5_keys keys='consensus_matrix_cluster_0,
+                                        consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom,
                                         consensus_matrix_cluster_0/bins/end, consensus_matrix_cluster_0/bins/start,
-                                        consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length, 
-                                        consensus_matrix_cluster_0/chroms/name, consensus_matrix_cluster_0/indexes, 
+                                        consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length,
+                                        consensus_matrix_cluster_0/chroms/name, consensus_matrix_cluster_0/indexes,
                                         consensus_matrix_cluster_0/indexes/bin1_offset, consensus_matrix_cluster_0/indexes/chrom_offset,
                                         consensus_matrix_cluster_0/pixels, consensus_matrix_cluster_0/pixels/bin1_id,
-                                        consensus_matrix_cluster_0/pixels/bin2_id, consensus_matrix_cluster_0/pixels/count, 
-                                        consensus_matrix_cluster_1, consensus_matrix_cluster_1/bins, consensus_matrix_cluster_1/bins/chrom, 
+                                        consensus_matrix_cluster_0/pixels/bin2_id, consensus_matrix_cluster_0/pixels/count,
+                                        consensus_matrix_cluster_1, consensus_matrix_cluster_1/bins, consensus_matrix_cluster_1/bins/chrom,
                                         consensus_matrix_cluster_1/bins/end, consensus_matrix_cluster_1/bins/start, consensus_matrix_cluster_1/chroms,
                                         consensus_matrix_cluster_1/chroms/length, consensus_matrix_cluster_1/chroms/name, consensus_matrix_cluster_1/indexes,
-                                        consensus_matrix_cluster_1/indexes/bin1_offset, consensus_matrix_cluster_1/indexes/chrom_offset, 
+                                        consensus_matrix_cluster_1/indexes/bin1_offset, consensus_matrix_cluster_1/indexes/chrom_offset,
                                         consensus_matrix_cluster_1/pixels, consensus_matrix_cluster_1/pixels/bin1_id, consensus_matrix_cluster_1/pixels/bin2_id,
-                                        consensus_matrix_cluster_1/pixels/count, consensus_matrix_cluster_2, consensus_matrix_cluster_2/bins, 
-                                        consensus_matrix_cluster_2/bins/chrom, consensus_matrix_cluster_2/bins/end, consensus_matrix_cluster_2/bins/start, 
+                                        consensus_matrix_cluster_1/pixels/count, consensus_matrix_cluster_2, consensus_matrix_cluster_2/bins,
+                                        consensus_matrix_cluster_2/bins/chrom, consensus_matrix_cluster_2/bins/end, consensus_matrix_cluster_2/bins/start,
                                         consensus_matrix_cluster_2/chroms, consensus_matrix_cluster_2/chroms/length, consensus_matrix_cluster_2/chroms/name,
-                                        consensus_matrix_cluster_2/indexes, consensus_matrix_cluster_2/indexes/bin1_offset, consensus_matrix_cluster_2/indexes/chrom_offset, 
-                                        consensus_matrix_cluster_2/pixels, consensus_matrix_cluster_2/pixels/bin1_id, consensus_matrix_cluster_2/pixels/bin2_id, 
+                                        consensus_matrix_cluster_2/indexes, consensus_matrix_cluster_2/indexes/bin1_offset, consensus_matrix_cluster_2/indexes/chrom_offset,
+                                        consensus_matrix_cluster_2/pixels, consensus_matrix_cluster_2/pixels/bin1_id, consensus_matrix_cluster_2/pixels/bin2_id,
                                         consensus_matrix_cluster_2/pixels/count'/>
                 </assert_contents>
             </output>
         </test>
-       
+
     </tests>
     <help><![CDATA[