--- a/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/build/tools/GetGenesFromReactions/GetGenesFromReactions.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.5.0">
-  <description>Get gene lists from a list of reactions and a GSMN.</description>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="develop">
+  <description>Get gene lists from a list of reactions and a SBML file.</description>
   <xrefs>
     <xref type="bio.tools">met4j</xref>
   </xrefs>
   <requirements>
-    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
  -r "$reactionFile"
@@ -34,17 +34,127 @@
   </outputs>
   <tests>
     <test>
-    <param name="sbml" value="XF_network.sbml"/>
-    <param name="reactionFile" value="XF_network_R_Seed.tab"/>
-    <output ftype="tsv" name="outputFile">
-      <assert_contents>
-        <has_n_lines n="2"/>
-        <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
-        <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
-      </assert_contents>
-    </output>
-  </test>
+                                                                      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="sbml" value="XF_network.sbml"/>
+                                                                      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
+                                                                      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <output ftype="tsv" name="outputFile">
+                                                                                              
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="2"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
+                                                                                                                    
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                            
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    </test>
   </tests>
-  <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
+  <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
   <citations/>
 </tool>