--- a/tools/convert/Sbml2Tab/Sbml2Tab.xml	Wed Jul 26 15:33:45 2023 +0000
+++ b/tools/convert/Sbml2Tab/Sbml2Tab.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -1,63 +1,305 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="MET4J_VERSION_TEST">
-  <description>Create a tabulated file from a SBML file</description>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="develop">
+  <description>Create a tabulated file listing reaction attributes from 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:MET4J_VERSION_TEST</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 convert.Sbml2Tab#if str($i):
- -i "$i"
+ -irr "$i"
 #end if
 #if str($r):
- -r "$r"
+ -rev "$r"
 #end if
- -in "$in"
- -out "$out"
+ -i "$in"
+ -o "$out"
 ]]></command>
   <inputs>
-    <param argument="-i" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
+    <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
+    <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
       <sanitizer invalid_char="_">
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
-    <param argument="-in" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
+    <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
   </inputs>
   <outputs>
     <data format="tsv" name="out"/>
   </outputs>
   <tests>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="in" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="tsv" name="out">
-      <assert_contents>
-        <has_n_lines n="8"/>
-        <has_n_columns n="9"/>
-        <has_text text="2.0 E[c] --&gt; D[c]"/>
-        <has_text text="A[c] &lt;==&gt; B[c]"/>
-      </assert_contents>
-    </output>
+                                                                                              
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="8"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="9"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_text text="2.0 E[c] --&gt; D[c]"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_text text="A[c] &lt;==&gt; B[c]"/>
+                                                                                                                    
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                            
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
     <test>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="in" value="toy_model.xml"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="i" value="-&gt;"/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <param name="r" value="="/>
+                                                                        
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
       <output ftype="tsv" name="out">
-      <assert_contents>
-        <has_n_lines n="8"/>
-        <has_n_columns n="9"/>
-        <has_text text="2.0 E[c] -&gt; D[c]"/>
-        <has_text text="A[c] = B[c]"/>
-      </assert_contents>
-    </output>
+                                                                                              
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_lines n="8"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_n_columns n="9"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_text text="2.0 E[c] -&gt; D[c]"/>
+                                                                                                                      
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          
+          <has_text text="A[c] = B[c]"/>
+                                                                                                                    
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                                                            
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </output>
+                                                                      
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
     </test>
   </tests>
-  <help><![CDATA[Create a tabulated file from a SBML file]]></help>
+  <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help>
   <citations/>
 </tool>