annotate COBRAxy/src/exportMetabolicModel.xml @ 548:5aef7b860706 draft default tip

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<tool id="exportMetabolicModel" name="Export Metabolic Model" version="1.0.0">
    <description>Export a tabular model to file format (SBML, JSON, MAT or YAML)</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__/exportMetabolicModel.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="Model tabular:"/>
        <param name="model_name" type="text" value="Converted_Model" label="Output model name:" help="Name for the created COBRA model"/>
        <param name="format" type="select" label="Output 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="Export Metabolic Model - 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 exports a tabular dataset into a standard metabolic model file formats using COBRApy.

**Input**
- A tabular/CSV/TSV file describing the metabolic properties of the model (reactions, metabolites, and genes), as generated by the Import Metabolic Model tool.

The possible columns are:
    - ReactionID: unique identifier of the reactions
    - Formula: chemical equation showing the metabolites involved in the reaction and their stoichiometric coefficients.
    - GPR: gene-protein-reaction association, expressed as a logical rule describing how genes contribute to catalyzing the reaction.
    - lower bound: minimum allowable flux value for the reaction.
    - upper bound: maximum allowable flux value for the reaction.
    - Objective coefficient: coefficient used in the objective function (e.g., for pFBA or FVA analyses).
    - Pathway_1,Pathway_2,etc.: possible pathways in which the reaction is involved.
    - InMedium: TRUE if the reaction represents nutrient uptake from the medium, FALSE otherwise.

Columns ReactionID and Formula are mandatory.

**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>