<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"/>

    <command detect_errors="exit_code">
      <![CDATA[
        python '$__tool_directory__/bakta_build_database.py'
        '$output_file'
        --database_version '$database_select'
        #if '$test_data_manager' != ''
            '$test_data_manager'
        #end if
      ]]></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>
        </param>
        <param name="test_data_manager" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- Test download -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" 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>