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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d
author recetox
date Tue, 16 Apr 2024 11:29:11 +0000
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children c4835715c7ac
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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1 <macros>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2 <token name="@HELP_matchms@">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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3 Documentation
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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4 The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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5 For an overview of the different galaxy modules, see the figure below.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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6 For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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7 and https://matchms.readthedocs.io/en/latest/ for the Python API.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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8
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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9 To get more familiar with the library, there is a `tutorial`_ available which explains how to build a mass spectrometry data processing
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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10 pipeline with matchms.
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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12 .. _tutorial: https://medium.com/escience-center/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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14 Overview
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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15 .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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16 :width: 3120
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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17 :height: 1686
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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18 :scale: 30
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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19 :alt: Overview of different matchms galaxytools and how they are connected.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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20 </token>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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21 <token name="@HELP_matchms_networking@">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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22 <![CDATA[
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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23 Documentation
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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24 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
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25 and https://matchms.readthedocs.io/en/latest/.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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27 **Upstream Tools**
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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29 matchms similarity
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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31 **Downstream Tools**
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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33 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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34 ]]>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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35 </token>
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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37 <token name="@HELP_formatter@">
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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38 <![CDATA[
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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39 Usage
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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40 This tool creates user friendly tables from the similarity scores produced by **matchms similarity**.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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41 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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43 Input Table Format
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44 The tool expects a JSON file containing serialized matchms Scores object.
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46 Output Table Format
2b61ec493df6 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a0565620150b69e0ca87aa686709c25356436f71
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47 +----------+-----------+---------+--------+
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48 | query | reference | matches | scores |
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49 +==========+===========+=========+========+
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50 | C001 | Glycine | 6 | 0.5 |
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51 +----------+-----------+---------+--------+
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52 | C002 | Glycine | 3 | 0.34 |
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53 +----------+-----------+---------+--------+
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54 | ... | ... | ... | ... |
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55 +----------+-----------+---------+--------+
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56 ]]>
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57 </token>
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58 </macros>