annotate COBRAxy/tabular2MetabolicModel.xml @ 516:7726a4a7173f draft

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<tool id="tabular2MetabolicModel" name="tabular2MetabolicModel" version="1.0.0">
    <description>Convert a tabular dataset to a COBRA model</description>

    <!-- Python dependencies required for COBRApy -->
    <requirements>
        <requirement type="package" version="0.29.0">cobra</requirement>
        <requirement type="package" version="1.24.4">numpy</requirement>
        <requirement type="package" version="2.0.3">pandas</requirement>
        <requirement type="package" version="5.2.2">lxml</requirement>
    </requirements>

    <!-- Import shared macros if available -->
    <macros>
        <import>marea_macros.xml</import>
    </macros>

    <!-- Command to run the Python script -->
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/tabular2MetabolicModel.py
            --tool_dir $__tool_directory__
            --input $input 
            --format $format
            --output $output
            --out_log $log
    ]]></command>

    <!-- Tool inputs -->
    <inputs>
        <param name="input" type="data" format="tabular,csv,tsv" label="Input table"/>
        <param name="model_name" type="text" value="Converted_Model" label="Model name" help="Name for the created COBRA model"/>
        <param name="format" type="select" label="Output COBRA model format">
            <option value="sbml" selected="true">SBML (.xml)</option>
            <option value="json">JSON (.json)</option>
            <option value="mat">MATLAB (.mat)</option>
            <option value="yaml">YAML (.yml)</option>
        </param>
    </inputs>

    <!-- Tool outputs -->
    <outputs>
        <data name="log" format="txt" label="Tabular to Model Conversion - Log" />
        <data name="output" format="xml" label="${model_name}.${format}">
            <change_format>
                <when input="format" value="sbml" format="xml"/>
                <when input="format" value="json" format="json"/>
                <when input="format" value="mat" format="mat"/>
                <when input="format" value="yaml" format="yaml"/>
            </change_format>
        </data>
    </outputs>

    <!-- Help section -->
    <help><![CDATA[
This tool converts a tabular dataset into a COBRA model using COBRApy.

**Input**
- A tabular/CSV/TSV file describing reactions, metabolites, or stoichiometry.

**Output**
- A COBRA model in the chosen format:  
  - SBML (.xml)  
  - JSON (.json)  
  - MATLAB (.mat)  
  - YAML (.yml)  

**Notes**
- The exact table structure (columns required) depends on how you want to encode reactions and metabolites.  
- You can extend the Python script to parse specific column formats.  
    ]]></help>
</tool>