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view data_manager/bakta_build_database.xml @ 6:3b9969001f3f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 2fa443ab6c1b3513a585123edd2cdf864e5123ae-dirty
author pimarin
date Thu, 27 Oct 2022 15:07:44 +0000
parents b475dd46612e
children 47a3aac8fcf7
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<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_file' &&
        ln -s '$output_file' 'output_file/json_output' &&
        python '$__tool_directory__/bakta_build_database.py'
        './output_file/json_output'
        --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="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" selected="true" > 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_file/json_output"/>
    </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>