annotate help.xml @ 1:8e18dcf410ec draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ed583a475c54aa862cf7628edd232305e8582df3

<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.

            To get more familiar with the library, there is a `tutorial`_ available which explains how to build a mass spectrometry data processing
            pipeline with matchms.
                
            .. _tutorial: https://medium.com/escience-center/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee

        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>