--- a/marea_2/custom_data_generator.xml	Mon Aug 05 20:03:49 2024 +0000
+++ b/marea_2/custom_data_generator.xml	Mon Aug 05 20:04:01 2024 +0000
@@ -1,60 +1,62 @@
-<tool id="MaREA Custom Data Generator" name="CustomDataGenerator" version="2.0.0">
-    
-    <macros>
-        <import>marea_macros.xml</import>
-    </macros>
-
-	<requirements>
-        <requirement type="package" version="1.24.4">numpy</requirement>
-        <requirement type="package" version="2.0.3">pandas</requirement>
-		<requirement type="package" version="0.29.0">cobra</requirement>
-        <requirement type="package" version="5.2.2">lxml</requirement>
-	</requirements>
-
-    <command detect_errors="exit_code">
-        <![CDATA[
-      	python $__tool_directory__/custom_data_generator.py
-        --input $input
-        --name $input.element_identifier
-        --out_log $log
-        --bounds $bounds
-        --reactions $reactions
-        --medium $medium
-        --rules $rules
-        ]]>
-    </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" />
-    </inputs>
-
-    <outputs>
-        <data format="txt" name="log" label="CustomDataGenerator - $name - Log" />
-        <data format="tabular" name="bounds" label="${tool.name}_Bounds" />
-        <data format="tabular" name="reactions" label="${tool.name}_Reactions" />
-        <data format="tabular" name="medium" label="${tool.name}_Medium" />
-        <data format="tabular" name="rules" label="${tool.name}_Rules" />
-    </outputs>
-
-    <help>
-    <![CDATA[
-What it does
--------------
-
-This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules.
-
-Accepted files:
-    - A model: JSON or XML file reporting reactions and rules contained in the model.   
-
-
-Output:
--------------
-
-The tool generates:
-    - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
-    - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
-    - a log file (.txt).
-    ]]>
-    </help>
-    <expand macro="citations" />
+<tool id="MaREA Custom Data Generator" name="CustomDataGenerator" version="2.0.0">
+    
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
+
+	<requirements>
+        <requirement type="package" version="1.24.4">numpy</requirement>
+        <requirement type="package" version="2.0.3">pandas</requirement>
+		<requirement type="package" version="0.29.0">cobra</requirement>
+        <requirement type="package" version="5.2.2">lxml</requirement>
+	</requirements>
+
+    <command detect_errors="exit_code">
+        <![CDATA[
+      	python $__tool_directory__/custom_data_generator.py
+        --input $input
+        --name $input.element_identifier
+        --output_format $output_format
+        --out_log $log
+        ]]>
+    </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>
+    </outputs>
+
+    <help>
+    <![CDATA[
+What it does
+-------------
+
+This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules.
+
+Accepted files:
+    - A model: JSON or XML file reporting reactions and rules contained in the model.   
+
+
+Output:
+-------------
+
+The tool generates:
+    - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
+    - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
+    - a log file (.txt).
+    ]]>
+    </help>
+    <expand macro="citations" />
 </tool>
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