changeset 3:b1f0a9b02efd 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 14:25:56 2023 +0000
+++ b/macros.xml	Thu Jul 31 16:45:18 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/scHicPlotConsensusMatrices.xml	Fri Apr 14 14:25:56 2023 +0000
+++ b/scHicPlotConsensusMatrices.xml	Thu Jul 31 16:45:18 2025 +0000
@@ -4,6 +4,7 @@
         <token name="@BINARY@">scHicPlotConsensusMatrices</token>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
@@ -13,13 +14,13 @@
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
             --chromosomes $chromosome
         #end if
-        
+
         #if $colormap:
             --colorMap $colormap
         #end if
         #if $dpi:
             --dpi $dpi
-        #end if 
+        #end if
         --outFileName plot.$image_file_format
 
         --threads @THREADS@
@@ -32,13 +33,13 @@
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
         <expand macro="colormap" />
         <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='Consensus matrix plot on ${on_string}'>
@@ -53,7 +54,7 @@
             <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
-            <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>        
+            <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>
         </test>
          <test>
             <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
@@ -61,9 +62,9 @@
             <param name="dpi" value="300" />
             <param name="chromosomes" value="chr1 chr2" />
 
-            <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>        
+            <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/>
         </test>
-       
+
     </tests>
     <help><![CDATA[
 
@@ -81,4 +82,4 @@
 ]]></help>
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>