<tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> Bakta database builder </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>

    <command detect_errors="aggressive"><![CDATA[
        mkdir './output_dir_json' &&
        ln -s '$output_file' './output_dir_json/json_output.json' &&
        python '$__tool_directory__/bakta_build_database.py'
        './output_dir_json/json_output.json'
        --database_version '$database_select'
    ]]></command>
    <inputs>
        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)" >
            <option value="latest" selected="true" > Latest available version </option>
            <option value="1.0"> V1.0_2020-11-20 </option>
            <option value="1.1"> V1.1_2020-12-18 </option>
            <option value="2.0"> V2.0_2021-04-05 </option>
            <option value="3.0"> V3.0_2021-08-05 </option>
            <option value="3.1"> V3.1_2022-02-03  </option>
            <option value="4.0"> V4.0_2022-08-29 </option>
            <option value="test"> database_test </option>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json" from_work_dir="./output_dir_json/json_output.json"/>
    </outputs>
    <tests>
        <!-- Test download -->
        <test expect_num_outputs="1">
            <param name="database_select" value="test"/>
            <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
        </test>
    </tests>
    <help><![CDATA[
        Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
    ]]></help>
    <citations>
        <citation type="doi">10.1099/mgen.0.000685</citation>
    </citations>
</tool>