changeset 3:74e28c7ca918 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b

--- a/macros.xml	Fri Apr 14 14:26:40 2023 +0000
+++ b/macros.xml	Thu Jul 31 16:48:11 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>

--- a/scHicClusterMinHash.xml	Fri Apr 14 14:26:40 2023 +0000
+++ b/scHicClusterMinHash.xml	Thu Jul 31 16:48:11 2025 +0000
@@ -4,6 +4,7 @@
         <token name="@BINARY@">scHicClusterMinHash</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
@@ -32,16 +33,16 @@
 
     ]]></command>
     <inputs>
-        
+
         <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>
         </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="numberOfHashFunctions" type="integer" value="800"  label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' />   
-        <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="numberOfHashFunctions" type="integer" value="800"  label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' />
+        <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'/>
         <param name='exactModeMinhash' type='boolean' truevalue='--exactModeMinHash' label='The MinHash algorithm computes additional the exact euclidean distance.'/>
@@ -73,7 +74,7 @@
             <param name='numberOfClusters' value='3' />
             <param name='numberOfHashFunctions' value='800' />
             <param name='exactModeMinhash' value='true' />
-            
+
             <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans_exact.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
         <test>
@@ -83,11 +84,11 @@
             <param name='numberOfHashFunctions' value='800' />
             <param name='chromosomes' value='chr1 chr2' />
 
-            
+
             <output name="outFileName" file="scHicClusterMinHash/cluster_spectral_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
 
-        
+
     </tests>
     <help><![CDATA[