view data_manager/busco_options.xml @ 6:709faa13c793 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 68696449a909c43d0e44bc9cfc8f8945e8a9dfce

<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <description></description>
        <macros>
        <token name="@TOOL_VERSION@">5.8.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $test:
            busco --download_path test/ --download virus > /dev/null &&
            #set db_path="./test"
        #else
            #set db_path=$cached_db.fields.path
        #end if
        python '$__tool_directory__/extract.py' '$db_path' '$cached_db' '$out_file'
    ]]></command>
    <inputs>
        <param name="test" type="hidden"/>
        <param name="cached_db" label="Cached database with lineage" type="select">
            <options from_data_table="busco_database">
                <validator message="No BUSCO database is available" type="no_options"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="BUSCO options data manager: JSON"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="test" value="true"/>
            <param name="cached_db" value="test"/>
            <output name="out_file">
                <assert_contents>
                    <has_text text="busco_database_options"/>
                    <has_text text="Chordopoxvirinae"/>
                    <has_text text="chordopoxvirinae_"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>This tool determines the possible choices of BUSCO lineages in a given BUSCO DB.</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btv351</citation>
    </citations>
</tool>