<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
        --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 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 or pickle.
    - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
    - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv or pickle.
    - medium composition: reporting the list of exchange/transport reactions. Format: csv or pickle.
    - a log file (.txt).
    ]]>
    </help>
    <expand macro="citations" />
</tool>