<tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0">
    <macros>
        <import>xmsannotator_macros.xml</import>
    </macros>

    <requirements>
        <container type="docker">@DOCKER_IMAGE@</container>
    </requirements>

    <command detect_errors="aggressive"><![CDATA[
        Rscript -e 'annotation <- xmsannotator::simple_annotation(
                        peaks = xmsannotator::load_hdf("$peaks", "peaks"),
                        adducts = xmsannotator::load_hdf("$adducts", "adducts"),
                        compounds = xmsannotator::load_hdf("$compounds", "compounds"),
                        mass_tolerance = 1e-6 * $mz_tolerance_ppm
                   )'
                -e 'xmsannotator::save_hdf("$annotation", "annotation", annotation)'
    ]]></command>

    <inputs>
        <expand macro="annotation"/>
    </inputs>

    <outputs>
        <data format="h5" name="annotation"/>
    </outputs>

    <help><![CDATA[
        Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database.

        The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks.
        A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance.
    ]]></help>

    <expand macro="citations"/>
</tool>