diff build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml @ 11:40c15b7467f1 draft default tip

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518

--- a/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml	Mon Feb 03 15:59:46 2025 +0000
+++ b/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml	Thu Feb 13 15:08:22 2025 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0">
+<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.1">
   <description>Advanced creation of a compound graph representation of a SBML file content</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath"
 #if str($inputSide) != 'None':
@@ -54,31 +54,56 @@
   </outputs>
   <tests>
     <test>
+            
       <param name="inputPath" value="XF_network.sbml"/>
+            
       <param name="inputSide" value="XF_network_C_Side.tab"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_line_matching expression=".*node.*" n="1101"/>
+                    
           <has_line_matching expression=".*edge.*" n="5581"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
     <test>
+            
       <param name="inputPath" value="XF_network.sbml"/>
+            
       <param name="inputSide" value="XF_network_C_Side.tab"/>
+            
       <param name="undirected" value="true"/>
+            
       <param name="computeWeight" value="true"/>
+            
       <param name="removeIsolated" value="true"/>
+            
       <param name="degree" value="true"/>
+            
       <param name="mergingStrat" value="by_id"/>
+            
       <param name="format" value="gml"/>
+            
       <output name="output">
+                
         <assert_contents>
+                    
           <has_line_matching expression=".*node.*" n="793"/>
+                    
           <has_line_matching expression=".*edge.*" n="9372"/>
+                  
         </assert_contents>
+              
       </output>
+          
     </test>
   </tests>
   <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.