<macros>
    <token name="@TOOL_VERSION@">0.11.0</token>

    <xml name="creator">
        <creator>
            <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
                name="RECETOX MUNI" />
        </creator>
    </xml>

    <token name="@HELP_matchms@">
        <![CDATA[
            Documentation
                For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
                and https://matchms.readthedocs.io/en/latest/.

            Upstream Tools
                +-----------+---------------+--------+-----------+
                | Name      | Output File   | Format | Parameter |
                +===========+===============+========+===========+
                | RAMClustR | Mass spectra  | msp    | references|
                +-----------+---------------+--------+-----------+
                | RAMClustR | Mass spectra  | msp    | queries   |
                +-----------+---------------+--------+-----------+

            Downstream Tools
                The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
        ]]>
    </token>

    <token name="@HELP_formatter@">
        <![CDATA[
            Usage
                This tool creates user friendly tables from the data matrices produces by matchms.
                The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.

            Input Table Format
                The tool expects two data matrices with the format as depicted below.
                The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).

                +----------+------+------+-----+
                |          | C001 | C002 | ... |
                +==========+======+======+=====+
                | Perylene | 0.1  | 0.0  | ... |
                +----------+------+------+-----+
                | Glycine  | 0.5  | 0.34 | ... |
                +----------+------+------+-----+
                |   ...    | ...  | ...  | ... |
                +----------+------+------+-----+

            Output Table Format
                +----------+-----------+---------+--------+
                | query    | reference | matches | scores |
                +==========+===========+=========+========+
                | C001     | Glycine   |      6  | 0.5    |
                +----------+-----------+---------+--------+
                | C002     | Glycine   |     3   | 0.34   |
                +----------+-----------+---------+--------+
                |   ...    | ...       | ...     | ...    |
                +----------+-----------+---------+--------+
        ]]>
    </token>
</macros>