annotate data_manager/data_manager_build_amrfinderplus.xml @ 0:eea0c38a9afd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19

<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="latest" selected="true">Latest available version</option>
                <option value="3.10">V3.10</option>
                <option value="3.9">V3.9</option>
                <option value="3.8">V3.8</option>
                <option value="3.6">V3.6</option>
            </param>
            <when value="latest">
            </when>
            <when value="3.10">
                <param name="database_date_select" type="select" label="Date version">
                <option value="2022-10-11.2" selected="true">2022-10-11.2</option>
                <option value="2022-08-09.1">2022-08-09.1</option>
                <option value="2022-05-26.1">2022-05-26.1</option>
                <option value="2022-04-04.1">2022-04-04.1</option>
                <option value="2021-12-21.1">2021-12-21.1</option>
                <option value="2021-09-30.1">2021-09-30.1</option>
                <option value="2021-09-30.1">2021-08-11.1</option>
                <option value="2021-09-30.1">2021-06-01.1</option>
                <option value="2021-09-30.1">2021-03-01.1</option>
                </param>
            </when>
            <when value="3.9">
                <param name="database_date_select" type="select" label="Date version">
                <option value="2020-11-09.1" selected="true">2020-11-09.1</option>
                <option value="2020-12-17.1">2020-12-17.1</option>
                </param>
            </when>
             <when value="3.8">
                <param name="database_date_select" type="select" label="Date version">
                <option value="2020-09-30.1" selected="true">2020-09-30.1</option>
                <option value="2020-09-22.2">2020-09-22.2</option>
                <option value="2020-07-16.2">2020-07-16.2</option>
                <option value="2020-06-11.1">2020-06-11.1</option>
                <option value="2020-05-04.1">2020-05-04.1</option>
                </param>
            </when>
            <when value="3.6">
                <param name="database_date_select" type="select" label="Date version">
                <option value="2020-01-22.1" selected="true">2020-01-22.1</option>
                <option value="2020-03-20.1">2020-03-20.1</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" value="amrfinderplus_test_data_manager_1.json"/>
        </test>
        <!-- Test_2 DB 3.2 -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test"/>
            <conditional name="database_list">
                <param name="database_version_select" value="3.6"/>
                <param name="database_date_select" value="2020-03-20.1"/>
            </conditional>
            <output name="output_file" value="amrfinderplus_test_data_manager_2.json"/>
        </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>