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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 129488bfd91735fc55fe32edb1079c24eee7b2d3
author recetox
date Thu, 14 Nov 2024 15:09:15 +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
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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4 The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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5 For an overview of the different galaxy modules, see the figure below.
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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6 For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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7 and https://matchms.readthedocs.io/en/latest/ for the Python API.
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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9 Overview
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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10 .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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11 :width: 3120
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12 :height: 1686
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13 :scale: 30
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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14 :alt: Overview of different matchms galaxytools and how they are connected.
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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15 </token>
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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16 <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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17 <![CDATA[
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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18 Documentation
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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19 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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20 and https://matchms.readthedocs.io/en/latest/.
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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22 **Upstream Tools**
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23
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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24 matchms similarity
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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26 **Downstream Tools**
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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28 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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29 ]]>
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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30 </token>
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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32 <token name="@HELP_formatter@">
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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33 <![CDATA[
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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34 Usage
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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35 This tool creates user friendly tables from the similarity scores produced by **matchms similarity**.
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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36 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
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37
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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38 Input Table Format
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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39 The tool expects a JSON file containing serialized matchms Scores object.
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40
107186a6fcec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f5f5a8eff32c9b5de792dce99bc3c63dc971e82c
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41 Output Table Format
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42 +----------+-----------+---------+--------+
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43 | query | reference | matches | scores |
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44 +==========+===========+=========+========+
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45 | C001 | Glycine | 6 | 0.5 |
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46 +----------+-----------+---------+--------+
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47 | C002 | Glycine | 3 | 0.34 |
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48 +----------+-----------+---------+--------+
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49 | ... | ... | ... | ... |
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50 +----------+-----------+---------+--------+
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51 ]]>
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52 </token>
13
6e965d099233 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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53 </macros>