<tool id="recetox_xmsannotator_simple" name="RECETOX xMSannotator simple" version="@TOOL_VERSION@+galaxy0">
    <description>annotate peak intensity table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <expand macro="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[
        @HELP@
        ]]>
    </help>

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