annotate help.xml @ 3:d50ce2f51fc0 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 129488bfd91735fc55fe32edb1079c24eee7b2d3

<macros>
    <token name="@HELP_matchms@">
        Documentation
            The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
            For an overview of the different galaxy modules, see the figure below.
            For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst
            and https://matchms.readthedocs.io/en/latest/ for the Python API.

        Overview
            .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
               :width: 3120
               :height: 1686
               :scale: 30
               :alt: Overview of different matchms galaxytools and how they are connected.
    </token>
    <token name="@HELP_matchms_networking@">
        <![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**

        matchms similarity
        
        **Downstream Tools**
        
        The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
        ]]>
    </token>
    
    <token name="@HELP_formatter@">
        <![CDATA[
            Usage
                This tool creates user friendly tables from the similarity scores produced by **matchms similarity**.
                The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.

            Input Table Format
                The tool expects a JSON file containing serialized matchms Scores object.

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