--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/custom_data_generator.xml	Sun Oct 13 11:41:34 2024 +0000
@@ -0,0 +1,63 @@
+<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>
+        <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
+        --out_rules $rules
+        --out_reactions $reactions
+        --out_bounds $bounds
+        --out_medium $medium
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
+        <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="${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>
+    <![CDATA[
+What it does
+-------------
+
+This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
+Reactions and rules can be used as inputs for the RAS and RPS generator tools.
+
+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 (tab separated).
+    - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
+    - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
+    - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
+    - a log file (.txt).
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
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