annotate data_manager/funannotate_options.xml @ 5:5459ec34767a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

<tool id="data_manager_funannotate_options" name="Funannotate options data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
    <macros>
        <token name="@TOOL_VERSION@">1.8.15</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $test:
            funannotate setup -d ./test/ -i busco busco_outgroups -b eukaryota > /dev/null &&
            #set db_path="./test"
        #else
            #set db_path=$database.fields.path
        #end if
        python '$__tool_directory__/extract.py' '$db_path' '$database' '$output_file'
    ]]></command>
    <inputs>
        <param name="test" type="hidden" value="" help="Used for testing"/>
        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />
                <filter type="sort_by" column="0" reverse_sort_order="true"/>
                <!-- <filter type="static_value" column="2" value="1.0" /> -->
            </options>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="test" value="true"/>
            <param name="database" value="test"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="busco_db" n="1"/>
                    <has_text text="outgroup" n="6"/>
                    <has_text text="trained_species" n="166"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_line line="1 x busco_db"/>
                <has_line line="166 x trained_species"/>
                <has_line line="6 x outgroup"/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
        This data managers determines the options available in the select parameters of the funannotate tool
        for a given funannotate DB in the funannotate data table

        .. _funannotate: https://funannotate.readthedocs.io
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.4054262</citation>
    </citations>
</tool>