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

    <expand macro="requirements"/>

    <command detect_errors="aggressive"><![CDATA[
        Rscript -e 'annotation <- xmsannotator::simple_annotation(
                        peaks = rhdf5::h5read("$peaks", "peaks"),
                        adducts = rhdf5::h5read("$adducts", "adducts"),
                        metabolites = rhdf5::h5read("$metabolites", "metabolites"),
                        mz_tolerance_ppm = as.double($mz_tolerance_ppm)
                   )'
                -e 'rhdf5::h5write(annotation, "$annotation", "annotation")'
    ]]></command>

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