changeset 3:0aca9bf1e402 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 14:23:35 2023 +0000
+++ b/macros.xml	Thu Jul 31 16:50:19 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/scHicPlotClusterProfiles.xml	Fri Apr 14 14:23:35 2023 +0000
+++ b/scHicPlotClusterProfiles.xml	Thu Jul 31 16:50:19 2025 +0000
@@ -4,6 +4,7 @@
         <token name="@BINARY@">scHicPlotClusterProfiles</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
@@ -14,7 +15,7 @@
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
             --chromosomes $chromosome
         #end if
-        
+
         #if $order_by_conditional.order_by_selection == 'orderByFile':
             --orderBy $order_by_conditional.order_by_selection
         #elif $order_by_conditional.order_by_selection == 'svl':
@@ -24,7 +25,7 @@
         #end if
         #if $dpi:
             --dpi $dpi
-        #end if 
+        #end if
         --outFileName plot.$image_file_format
 
         --threads @THREADS@
@@ -35,28 +36,28 @@
     <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'/>
-        <param name="maximalDistance" type="integer" value="2000000"  label="Maximal distance" help='Maximal distance to consider for plotting' />   
+        <param name="maximalDistance" type="integer" value="2000000"  label="Maximal distance" help='Maximal distance to consider for plotting' />
         <conditional name="order_by_conditional">
             <param name='order_by_selection' label='Order samples by' type='select'>
                 <option value='svl' selected='true'>Short vs long range ratio</option>
                 <option value='orderByFile'>Order by file</option>
             </param>
             <when value='svl' >
-                <param name="distanceShortRange" type="integer" value="2000000"  label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
-                <param name="distanceLongRange" type="integer" value="12000000"  label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
+                <param name="distanceShortRange" type="integer" value="2000000"  label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
+                <param name="distanceLongRange" type="integer" value="12000000"  label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />
             </when>
             <when value='orderByFile'>
             </when>
         </conditional>
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
         <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
-        
+
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
             <option value="svg">svg</option>
             <option value="pdf">pdf</option>
         </param>
-        
+
     </inputs>
     <outputs>
         <data name='output_plot' from_work_dir='plot' format='png' label='Cluster profile plot on ${on_string} '>
@@ -79,9 +80,9 @@
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
 
-            <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/>        
+            <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/>
         </test>
-       
+
     </tests>
     <help><![CDATA[
 
@@ -100,4 +101,4 @@
 ]]></help>
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>