# HG changeset patch
# User francesco_lapi
# Date 1757067967 0
# Node ID 75eb44e730d9ba632da343b352550ff298d00812
# Parent  cccbf259459e8c15d87e9f7b5a2c84e8aea12586
Uploaded

diff -r cccbf259459e -r 75eb44e730d9 COBRAxy/custom_data_generator.xml
--- a/COBRAxy/custom_data_generator.xml	Fri Sep 05 10:15:52 2025 +0000
+++ b/COBRAxy/custom_data_generator.xml	Fri Sep 05 10:26:07 2025 +0000
@@ -4,16 +4,16 @@
         <import>marea_macros.xml</import>
     </macros>
 
-    <requirements>
+	<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="0.29.0">cobra</requirement>
         <requirement type="package" version="5.2.2">lxml</requirement>
-    </requirements>
+	</requirements>
 
     <command detect_errors="exit_code">
         <![CDATA[
-        python $__tool_directory__/custom_data_generator.py
+      	python $__tool_directory__/custom_data_generator.py
         --tool_dir $__tool_directory__
         --medium_selector $cond_model.medium_selector
         #if $cond_model.model_selector == 'Custom_model'
@@ -32,12 +32,7 @@
     </command>
     <inputs>
         <conditional name="cond_model">
-            <param name="model_selector" argument="--model_selector" type="select" label="Model:">
-                <option value="HMRcore">HMRcore</option>
-                <option value="Recon">Recon 2.2</option>
-                <option value="ENGRO2"  selected="true">ENGRO 2</option>
-                <option value="Custom_model">Custom</option>
-            </param>
+            <expand macro="options_model"/>
             <!-- ENGRO2 -->
             <when value="ENGRO2">
                 <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
@@ -96,140 +91,12 @@
     </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"/>
-    </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, 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]
-
-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><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>
+        <data name="log" format="txt" label="CustomDataGenerator - Log" />
 
-    <command detect_errors="exit_code">
-        <![CDATA[
-        python $__tool_directory__/custom_data_generator.py
-        --tool_dir $__tool_directory__
-        --medium_selector $cond_model.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
-        #if $cond_model.medium_selector == 'Custom'
-            --medium $cond_model.medium
-        #end if
-        --out_log $log
-        --out_tabular $out_tabular
-        ]]>
-    </command>
-    <inputs>
-        <conditional name="cond_model">
-            <param name="model_selector" argument="--model_selector" type="select" label="Model:">
-                <option value="HMRcore">HMRcore</option>
-                <option value="Recon">Recon 2.2</option>
-                <option value="ENGRO2"  selected="true">ENGRO 2</option>
-                <option value="Custom_model">Custom</option>
-            </param>
-            <!-- ENGRO2 -->
-            <when value="ENGRO2">
-                <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
-                <conditional name="medium_selector">
-                    <expand macro="options_ras_to_bounds_medium"/>
-                    <when value="Custom">
-                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
-                    </when>
-                </conditional>
-            </when>
-
-            <!-- Recon -->
-            <when value="Recon">
-                <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
-                <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
-                <option value="Default" selected="true">Default (Recon built-in medium)</option>
-                <option value="Custom">Custom medium file</option>
-                </param>
-                <conditional name="medium_selector">
-                    <when value="Custom">
-                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
-                    </when>
-                </conditional>
-            </when>
-
-            <!-- HMRcore -->
-            <when value="HMRcore">
-                <param name="name" argument="--name" type="text" value="HMRcore" hidden="true" />
-                <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
-                <option value="Default" selected="true">Default (HMRcore built-in medium)</option>
-                <option value="Custom">Custom medium file</option>
-                </param>
-                <conditional name="medium_selector">
-                    <when value="Custom">
-                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
-                    </when>
-                </conditional>
-            </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" />
-                <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>
-                    <option value="Custom">Custom medium file (required)</option>
-                </param>
-                <conditional name="medium_selector">
-                    <when value="Custom">
-                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-
-    </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"/>
-    </outputs>
+        <data name="out_tabular" format="tabular"
+                label="${cond_model.model_selector}_data_tabular"
+                optional="true"/>
+        </outputs>
 
     <help>
     <![CDATA[