annotate data_manager/pharokka_db_fetcher.xml @ 1:50caca83e7c9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31

<?xml version="1.0"?>
<tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Fetches the DB required for phrokka</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />
    <expand macro="requirements" />
    <expand macro="version" />

    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}' 
        $test_data_manager
    ]]>
    </command>
    <inputs>
    <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />

    <!-- <param name="test_data_manager" type="text" value=""/> -->
    <param argument="--version" type="text" value="1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version. The default value is recommended."/>
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
    <tests>
    <test expect_num_outputs="1">
        <param name="test_data_manager" value="--test"/>
        <param name="version" value="v1.2.0"/>
        <output name="out_file">
                <assert_contents>
                    <has_text text="Pharokka DB version"/>
                    <has_text text="db_from_"/>
                    <has_text text="pharokka_db"/>
                    <has_text text="v1.2.0"/>
                </assert_contents>
        </output>
    </test>
    </tests>
    <help>
        <![CDATA[
        Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
        This data manager fetches the DB using the build-in tool download script.
        The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102
        ]]>
    </help>
    <expand macro="citations" />
    <expand macro="creator" />
</tool>