# HG changeset patch
# User francesco_lapi
# Date 1757024171 0
# Node ID 0ac89744208f21b084b5672474db7ecb0f7be075
# Parent  5725e5bcccf95af4e18c7447548f16b0950048bf
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diff -r 5725e5bcccf9 -r 0ac89744208f custom_data_generator.xml
--- a/custom_data_generator.xml	Thu Sep 04 22:10:56 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-<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
-        --medium_selector $cond_medium.medium_selector
-        --output_format $output_format
-        #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_medium.medium_selector == 'Custom'
-            --medium $cond_medium.medium
-        #end if
-        --out_log $log
-        --out_data $out_data
-        ]]>
-    </command>
-    <inputs>
-        <!-- modello -->
-        <conditional name="cond_model">
-            <expand macro="options_model"/>
-            <when value="Custom_model">
-                <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
-                <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" help="Default: CustomModel. Do not use spaces or special symbols." />
-            </when>
-        </conditional>
-
-        <!-- formato output -->
-        <param name="output_format" argument="--output_format" type="select" label="Output format:">
-            <option value="tabular" selected="true">CSV (tabular)</option>
-            <option value="xlsx">Excel (.xlsx)</option>
-        </param>
-
-        <!-- medium -->
-        <conditional name="cond_medium">
-            <expand macro="options_ras_to_bounds_medium"/>
-            <when value="Custom">
-                <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
-            </when>
-        </conditional> 
-    </inputs>
-
-    <outputs>
-        <data name="log" format="txt" label="CustomDataGenerator - Log" />
-        <data name="out_data" format="$output_format" label="${cond_model.model_selector}_data" />
-    </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. Supported compressed formats: .zip, .gz and .bz2 - Filename must end with .json.zip (.xml.zip), .json.gz (.xml.gz) or .json.bz2 (.xml.bz2) for JSON (XML) files.   
-
-
-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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