diff build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml @ 10:6a112eaf8f38 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95

--- a/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml	Fri Jan 31 18:28:53 2025 +0000
+++ b/build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml	Mon Feb 03 15:59:46 2025 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop">
+<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0">
   <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:develop</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CompoundGraph -i "$inputPath"
 #if str($inputSide) != 'None':
@@ -54,106 +54,31 @@
   </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.