--- a/COBRAxy/custom_data_generator.xml	Mon Sep 08 13:52:58 2025 +0000
+++ b/COBRAxy/custom_data_generator.xml	Mon Sep 08 14:44:15 2025 +0000
@@ -1,4 +1,8 @@
 <tool id="CustomDataGenerator" name="Custom Data Generator" version="2.0.0">
+    
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
 
 	<requirements>
         <requirement type="package" version="1.24.4">numpy</requirement>
@@ -7,88 +11,29 @@
         <requirement type="package" version="5.2.2">lxml</requirement>
 	</requirements>
 
-    <macros>
-        <import>marea_macros.xml</import>
-    </macros>
-
     <command detect_errors="exit_code">
         <![CDATA[
       	python $__tool_directory__/custom_data_generator.py
-        --tool_dir $__tool_directory__
-        --medium_selector $cond_model.cond_medium.medium_selector
-        #if $cond_model.model_selector == 'Custom_model'
-            --input $cond_model.input
-            --name $cond_model.name
-        #else
-            --model $cond_model.model_selector
-            --name $cond_model.model_selector
-        #end if
-
-        --gene_format $cond_model.gene_format
-        
+        --input $input
+        --name $input.element_identifier
         --out_log $log
-        --out_tabular $out_tabular
+        --out_rules $rules
+        --out_reactions $reactions
+        --out_bounds $bounds
+        --out_medium $medium
         ]]>
     </command>
     <inputs>
-        <conditional name="cond_model">
-            <expand macro="options_model"/>
-            
-            <!-- ENGRO2 -->
-            <when value="ENGRO2">
-                <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
-                <conditional name="cond_medium">
-                    <expand macro="options_ras_to_bounds_medium"/>
-                </conditional>
-
-                <param name="gene_format" argument="--gene_format" type="select" label="Gene nomenclature format:">
-                    <option value="Default" selected="true">Keep original gene nomenclature</option>
-                    <option value="ENSG">ENSNG (Ensembl Gene ID)</option>
-                    <option value="HGNC_symbol">HGNC Symbol</option>
-                    <option value="HGNC_ID">HGNC ID</option>
-                    <option value="entrez_id">Entrez Gene ID</option>
-                </param>
-            </when>
-
-            <!-- Recon -->
-            <when value="Recon">
-                <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
-                <conditional name="cond_medium">
-                    <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
-                        <option value="Default" selected="true">Default (Recon built-in medium)</option>
-                    </param>
-                    <when value="Default">
-                        <!-- Nessun parametro aggiuntivo necessario -->
-                    </when>
-                </conditional>
-                <param name="gene_format" argument="--gene_format" type="select" label="Gene nomenclature format:">
-                    <option value="Default" selected="true">Keep original gene nomenclature</option>
-                </param>
-            </when>
-
-            <!-- Custom model -->
-            <when value="Custom_model">
-                <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
-                <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" />
-                <conditional name="cond_medium">
-                    <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
-                        <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>
-                    </param>
-                    <when value="Default">
-                        <!-- Nessun parametro aggiuntivo necessario -->
-                    </when>
-                </conditional>
-                <param name="gene_format" argument="--gene_format" type="select" label="Gene nomenclature format:">
-                    <option value="Default" selected="true">Keep original gene nomenclature</option>
-                </param>
-            </when>
-        </conditional>
-
+        <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
+        <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
     </inputs>
 
     <outputs>
-        <data name="log" format="txt" label="CustomDataGenerator - Log" />
-        <data name="out_tabular" format="tabular" label="${cond_model.model_selector}_data_tabular" optional="true"/>
+        <data format="txt" name="log" label="${tool.name} - Log" />
+        <data format="tabular" name="rules" label="${name}_Rules" />
+        <data format="tabular" name="reactions" label="${name}_Reactions" />
+        <data format="tabular" name="bounds" label="${name}_Bounds" />
+        <data format="tabular" name="medium" label="${name}_Medium" />
     </outputs>
 
     <help>
@@ -100,7 +45,8 @@
 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
 
 Accepted files:
-    - A model: JSON, XML, MAT or YAML (.yml) file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2. Filename must follow the pattern: {model_name}.{extension}.[zip|gz|bz2]
+    - A model: JSON or XML file reporting reactions and rules contained in the model.   
+
 
 Output:
 -------------