annotate gem_extract_exchange.xml @ 0:d9893d41dd6a draft default tip

planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171

<tool id="gem_extract_exchange" name="Get exchange bounds" version="@VERSION@" profile="@PROFILE@">
    <description>
        of a GEM
    </description>
    <macros>
        <import>gem_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command_cobra"/>
    <command>
        python '$__tool_directory__/gem_extract_exchange.py'
            --cb_model_location '${cb_model_location}'
            -output '${output}'
    </command>
    <inputs>
        <expand macro="input_model"/>
    </inputs>
    <outputs>
        <expand macro="output"/>
    </outputs>
    <tests>
        <!-- Test 1: Valid minimal GEM model -->
        <test>
            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
            <output name="output" file="textbook_model_cobrapy_exchange.csv"/>
        </test>
        <!-- Test 2: Invalid model format -->
        <test expect_failure="true">
            <param name="cb_model_location" value="invalid_format.txt"/>
            <assert_stderr>
                <has_text text="The model could not be read"/>
            </assert_stderr>
        </test>
        <expand macro="test_invalid_model"/>
    </tests>
    <help><![CDATA[
        GEM Extract Exchange Bounds

        Overview

        This tool extracts the exchange reactions and their associated bounds from a Genome-scale Metabolic (GEM) model in SBML format. The extracted exchange reactions are saved in a CSV file for further analysis or modification. Exchange reactions represent interactions between the metabolic network and the external environment, often used to simulate fluxes of metabolites in and out of the system.

        Inputs

        - `Model to extract exchange for`: This should be an SBML file containing the GEM model. The tool will identify and extract only the exchange reactions (reactions responsible for importing/exporting metabolites).

        Outputs

        - `GEM exchange reactions`: A CSV file with the following columns:
        - `reaction_id`: The ID of the exchange reaction.
        - `reaction_name`: The name of the exchange reaction.
        - `reaction_stoichiometry`: The stoichiometry of the reaction.
        - `lower_bound`: The lower bound of the exchange flux (typically representing the uptake limit).
        - `upper_bound`: The upper bound of the exchange flux (typically representing the secretion limit).
    ]]></help>
    <citations>
        <expand macro="citation_cobrapy"/>
    </citations>
</tool>