annotate data_manager/data_manager_build_amrfinderplus.xml @ 2:a5921c09b7b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709

<tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>AMRFinderPlus database builder</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
      <![CDATA[
python '$__tool_directory__/data_manager_build_amrfinderplus.py'
    '$output_file'
    --db_version '$database_list.database_version_select'
    #if $database_list.database_version_select != 'latest':
    --db_date '$database_list.database_date_select'
    #end if
    $test_data_manager
      ]]></command>
    <inputs>
        <conditional name="database_list">
            <param name="database_version_select" type="select" label="Database version">
                <option value="3.12">V3.12</option>
            </param>
            <when value="3.12">
                <param name="database_date_select" type="select" label="Date version">
                    <option value="2024-05-02.2">2024-05-02.2</option>
                    <option value="2024-01-31.1">2024-01-31.1</option>
                </param>
            </when>
        </conditional>
         <param name="test_data_manager" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- Test_1 DB latest -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <output name="output_file">
                <assert_contents>
                    <has_n_lines n="1"/>
                    <has_text text="{&quot;data_tables&quot;"/>
                    <has_text text="amrfinderplus_versioned_database"/>
                    <has_text text='"db_version": "3.12"'/>
                </assert_contents>
            </output>
        </test>
        <!-- Test_2 DB 3.12 2024-01-31.1 -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <conditional name="database_list">
                <param name="database_version_select" value="3.12"/>
                <param name="database_date_select" value="2024-01-31.1"/>
            </conditional>
            <output name="output_file">
                <assert_contents>
                    <has_n_lines n="1"/>
                    <has_text text="{&quot;data_tables&quot;"/>
                    <has_text text="amrfinderplus_versioned_database"/>
                    <has_text text='"name": "V3.12-2024-01-31.1"'/>
                    <has_text text='"db_version": "3.12"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Download AMRFinderPlus database from the NCBI server
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41598-021-91456-0</citation>
    </citations>
</tool>