<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
    <requirements>
        <requirement type="package" version="1.8.9">funannotate</requirement>
        <requirement type="package" version="2.26.0">requests</requirement>
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command detect_errors="exit_code"><![CDATA[
#if $wget:
    ## Asked for wget, we assume there's a certificate problem on (at least) one
    ## of the many requested servers, force disable of all checks
    echo "check_certificate = off" > \$HOME/.wgetrc &&
#end if

python -u '$__tool_directory__/funannotate.py'
$partial_data
$wget
\$(date +'%Y-%m-%d-%H%M%S')
'funannotate'
'${output_file}'
    ]]></command>
    <inputs>
        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
        <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="partial_data" value="--partial"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="Funannotate database "/>
                    <has_text text='"format_version": "1.0"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="partial_data" value="--partial"/>
            <param name="wget" value="True"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="Funannotate database "/>
                    <has_text text='"format_version": "1.0"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        This data managers fetches data from various databases for the funannotate
        annotation tool and updates the funannotate data table.

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