Mercurial > repos > recetox > matchms

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
author recetox
date Tue, 02 May 2023 10:12:59 +0000
parents 4f16b5e561c4
children
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <macros>
16
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2 <token name="@TOOL_VERSION@">0.17.0</token>
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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3
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 <xml name="creator">
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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5 <creator>
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3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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6 <yield/>
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 <person
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 givenName="Helge"
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 familyName="Hecht"
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 url="https://github.com/hechth"
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11 identifier="0000-0001-6744-996X" />
13
cfa8b66fb106 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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12 <person
16
21413e40f9a5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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13 givenName="Maksym"
21413e40f9a5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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14 familyName="Skoryk"
21413e40f9a5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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15 url="https://github.com/maximskorik"
21413e40f9a5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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16 identifier="0000-0003-2056-8018" />
21413e40f9a5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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17 <person
13
cfa8b66fb106 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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18 givenName="Zargham"
cfa8b66fb106 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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19 familyName="Ahmad"
cfa8b66fb106 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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20 url="https://github.com/zargham-ahmad"
cfa8b66fb106 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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21 identifier="0000-0002-6096-224X" />
18
4f16b5e561c4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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22 <person
4f16b5e561c4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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23 givenName="Wudmir"
4f16b5e561c4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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24 familyName="Rojas"
4f16b5e561c4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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25 url="https://github.com/wverastegui"
4f16b5e561c4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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26 identifier="0000-0001-7036-9987" />
10
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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27 <organization
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 url="https://www.recetox.muni.cz/"
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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30 name="RECETOX MUNI" />
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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31 </creator>
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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32 </xml>
16
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33
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34 <token name="@HELP_matchms@">
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 <![CDATA[
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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36 Documentation
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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37 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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38 and https://matchms.readthedocs.io/en/latest/.
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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39
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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40 Upstream Tools
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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41 +-----------+---------------+--------+-----------+
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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42 | Name | Output File | Format | Parameter |
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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43 +===========+===============+========+===========+
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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44 | RAMClustR | Mass spectra | msp | references|
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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45 +-----------+---------------+--------+-----------+
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 | RAMClustR | Mass spectra | msp | queries |
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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47 +-----------+---------------+--------+-----------+
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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48
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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49 Downstream Tools
16
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50 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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51 ]]>
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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52 </token>
17
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3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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54 <token name="@HELP_matchms_networking@">
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55 <![CDATA[
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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56 Documentation
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57 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
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58 and https://matchms.readthedocs.io/en/latest/.
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59
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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60 **Upstream Tools**
10
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61
17
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62 matchMS similarity
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63
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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64 **Downstream Tools**
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65
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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66 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
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67 ]]>
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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68 </token>
3e693373c551 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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69
10
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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70 <token name="@HELP_formatter@">
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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71 <![CDATA[
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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72 Usage
16
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73 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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74 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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75
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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76 Input Table Format
16
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77 The tool expects a JSON file containing serialized matchMS Scores object.
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c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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78
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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79 Output Table Format
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80 +----------+-----------+---------+--------+
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81 | query | reference | matches | scores |
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82 +==========+===========+=========+========+
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83 | C001 | Glycine | 6 | 0.5 |
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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84 +----------+-----------+---------+--------+
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85 | C002 | Glycine | 3 | 0.34 |
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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86 +----------+-----------+---------+--------+
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87 | ... | ... | ... | ... |
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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88 +----------+-----------+---------+--------+
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89 ]]>
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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90 </token>
17
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92 <xml name="citations">
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93 <citations>
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94 <citation type="doi">10.5281/zenodo.7178586</citation>
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95 <citation type="doi">10.21105/joss.02411</citation>
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96 </citations>
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97 </xml>
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98
10
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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99 </macros>