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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit bd80a813fb2f01f22eed0c874f8911ce4d00762a
author recetox
date Mon, 30 Jun 2025 13:03:32 +0000
parents 6e965d099233
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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1 <macros>
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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2 <token name="@HELP_matchms@">
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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3 Documentation
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4 The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
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5 For an overview of the different galaxy modules, see the figure below.
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e23c14cee5a9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit bd80a813fb2f01f22eed0c874f8911ce4d00762a
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6 For detailed documentation on the tool, see https://matchms.readthedocs.io/en/latest/ for the Python API.
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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8 Overview
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9 .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
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10 :width: 3120
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11 :height: 1686
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12 :scale: 30
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13 :alt: Overview of different matchms galaxytools and how they are connected.
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14 </token>
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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15 <token name="@HELP_matchms_networking@">
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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16 <![CDATA[
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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17 Documentation
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e23c14cee5a9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit bd80a813fb2f01f22eed0c874f8911ce4d00762a
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18 For documentation on the tool see https://matchms.readthedocs.io/en/latest/.
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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20 **Upstream Tools**
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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22 matchms similarity
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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24 **Downstream Tools**
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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26 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
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27 ]]>
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28 </token>
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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30 <token name="@HELP_formatter@">
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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31 <![CDATA[
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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32 Usage
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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33 This tool creates user friendly tables from the similarity scores produced by **matchms similarity**.
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34 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
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36 Input Table Format
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37 The tool expects a JSON file containing serialized matchms Scores object.
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107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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39 Output Table Format
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40 +----------+-----------+---------+--------+
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41 | query | reference | matches | scores |
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42 +==========+===========+=========+========+
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43 | C001 | Glycine | 6 | 0.5 |
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44 +----------+-----------+---------+--------+
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45 | C002 | Glycine | 3 | 0.34 |
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46 +----------+-----------+---------+--------+
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47 | ... | ... | ... | ... |
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48 +----------+-----------+---------+--------+
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49 ]]>
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50 </token>
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51 </macros>