view data_manager/gtdbtk_database_installer.xml @ 0:629464b96c2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f

<tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">202</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">20.09</token>
    </macros>
    <requirements>
        <requirement type="package" version="3.10.2">python</requirement>
    </requirements>
    <command>
    <![CDATA[
        python '$__tool_directory__/gtdbtk_database_installer.py'
          --database_id '$database_id'
          --database_name '$database_name'
          --url '$url'
          --out_file '$out_file'
    ]]>
    </command>
    <inputs>
	    <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/>
        <param name="database_id" type="text" value="" label="Database id" help="This value must be unique with nNo whitespace allowed-use underscores"/>
        <param name="url" type="text" value="https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz" label="URL for downloading the selected version of the GTDB-Tk database"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <!-- Not actually installing a huge GTDB-Tk database -->
            <param name="database_id" value="release202"/>
            <param name="database_name" value="GTDB-Tk database release 202"/>
            <param name="url" value="https://data.gtdb.ecogenomic.org/releases/release202/202.0/VERSION"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="GTDB-Tk database release 202"/>
                    <has_text text="release202"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
    </help>
    <citations>
        <citation type="doi">doi.org/10.1038/s41587-020-0501-8</citation>
        <citation type="doi">dx.doi.org/10.1038/nbt.4229</citation>
    </citations>
</tool>