Mercurial > repos > recetox > matchms_spectral_similarity
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b797ce0fea5cb3d9a0cf0ec31a21f9b73f112b4e
author | recetox |
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date | Mon, 15 Jan 2024 12:29:39 +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>