<macros>
    <token name="@TOOL_VERSION@">0.9.0</token>
    <xml name="requirements">
        <requirements>
            <container type="docker">recetox/recetox-xmsannotator:october-conda0</container>
        </requirements>
    </xml>
    <xml name="creator">
        <creator>
            <organization
                url="https://www.recetox.muni.cz/"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    <xml name="inputs">
        <param name="peak_table" type="data" format="csv,parquet">
            <label>Peak table</label>
            <help><![CDATA[
                A peak-intensity table such as outputted from apLCMS.
                The file is required to contain the fields <em>mz</em> and <em>rt</em>.
                Columns for feature intensity in a sample have to start with <em>intensity</em>.

            ]]></help>
        </param>
        <param name="compound_table" type="data" format="csv,parquet">
            <label>Compound database</label>
            <help><![CDATA[
                Database of compounds according to which the annotation is performed.
                The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
            ]]></help>
        </param>
        <param name="adduct_table" type="data" format="csv,parquet" optional="true">
            <label>Adduct database (optional)</label>
            <help><![CDATA[
                Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
                The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
            ]]></help>
        </param>
        <param name="adduct_weights" type="data" format="csv" optional="true">
            <label>adduct_weights</label>
        </param>
    </xml>

    <xml name="outputs">
        <data name="annotation_parquet" format="parquet"/>
    </xml>

    <xml name="tolerance">
        <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
            <label>Mass tolerance [ppm]</label>
            <help>Mass tolerance in ppm for database matching.</help>
        </param>
        <yield/>
    </xml>
    <token name="@HELP@">
        <![CDATA[
        Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
        using advanced methods.

        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.
        ]]>
    </token>
    <xml name="citations">
        <citation type="doi">10.1021/acs.analchem.6b01214</citation>
    </xml>
</macros>