annotate data_manager/omamer.xml @ 0:e1502e4f8725 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a

<tool id="data_manager_omamer" name="OMAmer data manager" version="2.0.2" tool_type="manage_data" profile="20.01">
    <macros>
        <import>macros.xml</import>
    </macros>
    <version_command></version_command>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/omamer.py'
        --name '$name'
        --json '$output_file'
    ]]></command>
    <inputs>
        <param name="output_dir" type="text" label="Output Directory" value=""/>
        <param name="name" type="select" label="Database">
            <option value="Primates">Primates</option>
            <option value="Viridiplantae">Viridiplantae</option>
            <option value="Metazoa">Metazoa</option>
            <option value="LUCA">LUCA</option>
        </param>
    </inputs>
    
    <outputs>
        <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/>
    </outputs>

    <tests>
        <test>
            <param name="output_dir" value="test_galaxy"/>
            <param name="name" value="Primates"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="Primates-v2.0"/>
                    <has_text text="database_omamer"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
        This data manager retrieves data from various pre-built databases.

        .. _omamer: https://github.com/DessimozLab/omamer
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btab219</citation>
    </citations>
</tool>