Mercurial > repos > recetox > matchms_spectral_similarity
view help.xml @ 12:67f65bcc94bf draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76
author | recetox |
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date | Wed, 13 Mar 2024 10:20:15 +0000 |
parents | 9ff95a1a2705 |
children | ee35dcec350a |
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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. 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>