--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/convert/SbmlWizard/SbmlWizard.xml	Fri Jan 31 18:28:53 2025 +0000
@@ -0,0 +1,231 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="met4j_SbmlWizard" name="SbmlWizard" version="develop">
+  <description>General SBML model processing</description>
+  <xrefs>
+    <xref type="bio.tools">met4j</xref>
+  </xrefs>
+  <requirements>
+    <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.SbmlWizard -i "$inputPath"
+#if str($inputSide) != 'None':
+ -rc "$inputSide"
+#end if
+#if str($toKeepC) != 'None':
+ -kc "$toKeepC"
+#end if
+ $removeIsolated
+#if str($inputReactions) != 'None':
+ -rr "$inputReactions"
+#end if
+#if str($toKeepR) != 'None':
+ -kr "$toKeepR"
+#end if
+ $removeNoFlux
+#if str($mergingStrat):
+ -mc "$mergingStrat"
+#end if
+ $removeDuplicated
+#if str($exchangeCompToRemove):
+ -rEX "$exchangeCompToRemove"
+#end if
+ -o "$outputPath"
+]]></command>
+  <inputs>
+    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
+    <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/>
+    <param argument="-kc" format="txt" label="file containing identifiers of compounds to keep from the metabolic network" name="toKeepC" optional="true" type="data" value=""/>
+    <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
+    <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/>
+    <param argument="-kr" format="txt" label="file containing identifiers of reactions to keep from the metabolic network" name="toKeepR" optional="true" type="data" value=""/>
+    <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/>
+    <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. &quot;by_name&quot; can be used if names are consistent and unambiguous across compartments, &quot;by_id&quot; can be used if compartment suffix is present in compounds identifiers (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
+      <option selected="true" value="no">no</option>
+      <option value="by_name">by_name</option>
+      <option value="by_id">by_id</option>
+    </param>
+    <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
+    <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
+      <sanitizer invalid_char="_">
+        <valid initial="string.printable"/>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="sbml" name="outputPath"/>
+  </outputs>
+  <tests>
+    <test>
+                                    			
+      
+      
+      
+      
+      
+      <param name="inputPath" value="Human-GEM_pathways.xml"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeIsolated" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeNoFlux" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="mergingStrat" value="by_id"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeDuplicated" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="exchangeCompToRemove" value="s"/>
+                                    			
+      
+      
+      
+      
+      
+      <output ftype="sbml" name="outputPath">
+                                                				
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                            					
+          
+          
+          
+          
+          
+          <has_text text="&lt;/sbml&gt;"/>
+                                                            				
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                			
+      
+      
+      
+      
+      
+      </output>
+                                    		
+    
+    
+    
+    
+    
+    </test>
+    <test>
+                                    			
+      
+      
+      
+      
+      
+      <param name="inputPath" value="XF_network.sbml"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeIsolated" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeNoFlux" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="removeDuplicated" value="true"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="inputSide" value="XF_network_C_Side.tab"/>
+                                    			
+      
+      
+      
+      
+      
+      <param name="inputReactions" value="XF_network_R_Seed.tab"/>
+                                    			
+      
+      
+      
+      
+      
+      <output ftype="sbml" name="outputPath">
+                                                				
+        
+        
+        
+        
+        
+        <assert_contents>
+                                                            					
+          
+          
+          
+          
+          
+          <has_text text="&lt;/sbml&gt;"/>
+                                                            				
+        
+        
+        
+        
+        
+        </assert_contents>
+                                                			
+      
+      
+      
+      
+      
+      </output>
+                                    		
+    
+    
+    
+    
+    
+    </test>
+  </tests>
+  <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
+  <citations/>
+</tool>