<tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy3">
    <macros>
        <import>xmsannotator_macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <container type="docker">@DOCKER_IMAGE@</container>
    </requirements>

    <command detect_errors="aggressive"><![CDATA[
        Rscript $wrapper
    ]]></command>

    <configfiles>
        <configfile name="wrapper"><![CDATA[
            library(xmsannotator)

            annotation <- simple_annotation(
            #if $peak_table.is_of_type("h5")
                peak_table = load_peak_table_hdf("${peak_table}"),
            #elif $peak_table.is_of_type("parquet")
                peak_table = load_peak_table_parquet("${peak_table}"),
            #end if
                adduct_table = load_adduct_table_parquet("${adduct_table}"),
                compound_table = load_compound_table_parquet("${compound_table}"),
                mass_tolerance = 1e-6 * ${mass_tolerance_ppm}
            )

            save_parquet(data = annotation, file = "${annotation_parquet}")
        ]]></configfile>
    </configfiles>

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

    <outputs>
        <expand macro="outputs"/>
    </outputs>

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

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

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