view data_manager/bakta_build_database.xml @ 5:baceff842902 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2

<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'
    $test_data_manager
]]></command>
    <inputs>
        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
            <option value="5.1" selected="true">V5.1 (2024-01-19)</option>
            <option value="5.1_light">V5.1 light (2024-01-19)</option>
            <option value="5.0">V5.0 (2023-02-20)</option>
            <option value="5.0_light">V5.0 light (2023-02-20)</option>
            <option value="4.0">V4.0 (2022-08-29)</option>
            <option value="3.1">V3.1 (2022-02-03)</option>
            <option value="3.0">V3.0 (2021-08-05)</option>
            <option value="2.0">V2.0 (2021-04-05)</option>
            <option value="1.1">V1.1 (2020-12-18)</option>
            <option value="1.0">V1.0 (2020-11-20)</option>
        </param>
        <param name="test_data_manager" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- Test 1 with version 1.0 -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <param name="database_select" value="1.0"/>
            <output name="output_file" ftype="data_manager_json">
                <assert_contents>
                    <has_text text="data_tables"/>
                    <has_text text="bakta_database"/>
                    <has_text text="bakta_version"/>
                    <has_text text="V1.0_2022-10-12"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 2 with the latest option -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <param name="database_select" value="5.1_light"/>
            <output name="output_file" ftype="data_manager_json">
                <assert_contents>
                    <has_text text="data_tables"/>
                    <has_text text="bakta_database"/>
                    <has_text text="bakta_version"/>
                    <has_text text="V5.1light_2024-01-19"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 3 with light db -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <param name="database_select" value="5.0_light"/>
            <output name="output_file" ftype="data_manager_json">
                <assert_contents>
                    <has_text text="data_tables"/>
                    <has_text text="bakta_database"/>
                    <has_text text="bakta_version"/>
                    <has_text text="V5.0light_2023-06-08"/>
                </assert_contents>
            </output>
        </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>