--- a/COBRAxy/custom_data_generator.xml	Thu Sep 19 08:03:27 2024 +0000
+++ b/COBRAxy/custom_data_generator.xml	Thu Sep 19 08:03:37 2024 +0000
@@ -16,26 +16,24 @@
       	python $__tool_directory__/custom_data_generator.py
         --input $input
         --name $input.element_identifier
-        --output_format $output_format
         --out_log $log
+        --out_rules $rules
+        --out_reactions $reactions
+        --out_bounds $bounds
+        --out_medium $medium
         ]]>
     </command>
     <inputs>
         <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" />
-        
-        <param name="output_format" argument="--output_format" type="select" label="Output files format:">
-            <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
-            <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
-        </param>
     </inputs>
 
     <outputs>
-        <data format="txt" name="log" label="CustomDataGenerator - $name - Log" />
-        
-        <collection name="results" type="list" label="Custom Data Results ($output_format)">
-            <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
-        </collection>
+        <data format="txt" name="log" label="${tool.name} - Log" />
+        <data format="tabular" name="rules" label="${tool.name} - rules" />
+        <data format="tabular" name="reactions" label="${tool.name} - reactions" />
+        <data format="tabular" name="bounds" label="${tool.name} - bounds" />
+        <data format="tabular" name="medium" label="${tool.name} - medium" />
     </outputs>
 
     <help>