Mercurial > repos > recetox > matchms_split
view help.xml @ 20:446fddefcee7 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4
author | recetox |
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date | Tue, 04 Jun 2024 07:15:28 +0000 |
parents | 072c7a101da6 |
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<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>