annotate gem_macros.xml @ 0:d9893d41dd6a draft default tip

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

<macros>
    <!-- Tokens -->
    <token name="@VERSION@">0.29.1</token>
    <token name="@PROFILE@">23.0</token>
    
    <!-- Add version commands for different tools -->
    <xml name="version_command_cobra">
        <version_command>echo '@VERSION@'</version_command>
    </xml>
    
    <xml name="version_command_escher">
        <version_command>python -c 'from escher import __version__; print(__version__)'</version_command>
    </xml>

    <xml name="version_command_memote">
        <version_command>python -c 'from memote import __version__; print(__version__)'</version_command>
    </xml>
    
    <!-- Version command uses cobra requirement version -->
    <xml name="version_command">
        <version_command>echo '@VERSION@'</version_command>
    </xml>

    <!-- Setting cobra requirement to use version token -->
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">cobra</requirement>
            <requirement type="package" version="2.2.3">pandas</requirement>
            <requirement type="package" version="0.17.0">memote</requirement>
            <requirement type="package" version="1.7.3">escher</requirement>
        </requirements>
    </xml>

    <!-- Common inputs -->
    <xml name="input_model">
        <param format="sbml" name="cb_model_location" type="data" label="Model to analyze"/>
    </xml>

    <xml name="input_uptake_constraints">
        <param format="csv" name="uptake_constraints_file" type="data" label="Uptake constraints CSV file" optional="true"/>
    </xml>

    <!-- Common outputs -->
    <xml name="output">
        <data name="output" format="csv" label="${tool.name} on ${on_string}"/>
    </xml>

    <!-- Common test elements -->
    <xml name="test_invalid_model">
        <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>
    </xml>

    <!-- Citations -->
    <xml name="citation_cobrapy">
        <citation type="doi">10.1186/1752-0509-7-74</citation>
    </xml>

    <xml name="citation_pandas">
        <citation type="doi">10.5281/zenodo.3509134</citation>
    </xml>

    <xml name="citation_escher">
        <citation type="doi">10.1371/journal.pcbi.1004321</citation>
    </xml>

    <xml name="citation_memote">
        <citation type="doi">10.1038/s41587-020-0446-y</citation>
    </xml>

</macros>