Mercurial > repos > recetox > matchms_filtering

annotate macros.xml @ 5:97c405041116 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
author recetox
date Tue, 18 Oct 2022 10:59:10 +0000
parents a1eb173cab5d
children 282815b0c7bd
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2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <macros>
5
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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2 <token name="@TOOL_VERSION@">0.17.0</token>
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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3
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 <xml name="creator">
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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5 <creator>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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6 <person
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 givenName="Helge"
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 familyName="Hecht"
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 url="https://github.com/hechth"
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 identifier="0000-0001-6744-996X" />
4
a1eb173cab5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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11 <person
5
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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12 givenName="Maksym"
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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13 familyName="Skoryk"
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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14 url="https://github.com/maximskorik"
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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15 identifier="0000-0003-2056-8018" />
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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16 <person
4
a1eb173cab5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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17 givenName="Zargham"
a1eb173cab5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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18 familyName="Ahmad"
a1eb173cab5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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19 url="https://github.com/zargham-ahmad"
a1eb173cab5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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20 identifier="0000-0002-6096-224X" />
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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21 <organization
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 url="https://www.recetox.muni.cz/"
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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23 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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24 name="RECETOX MUNI" />
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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25 </creator>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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26 </xml>
5
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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27
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 <token name="@HELP_matchms@">
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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29 <![CDATA[
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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30 Documentation
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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31 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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32 and https://matchms.readthedocs.io/en/latest/.
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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33
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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34 Upstream Tools
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 +-----------+---------------+--------+-----------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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36 | Name | Output File | Format | Parameter |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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37 +===========+===============+========+===========+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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38 | RAMClustR | Mass spectra | msp | references|
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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39 +-----------+---------------+--------+-----------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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40 | RAMClustR | Mass spectra | msp | queries |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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41 +-----------+---------------+--------+-----------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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42
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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43 Downstream Tools
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97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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44 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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45 ]]>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 </token>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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47
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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48 <token name="@HELP_formatter@">
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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49 <![CDATA[
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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50 Usage
5
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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51 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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52 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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53
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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54 Input Table Format
5
97c405041116 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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55 The tool expects a JSON file containing serialized matchMS Scores object.
1
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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56
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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57 Output Table Format
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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58 +----------+-----------+---------+--------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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59 | query | reference | matches | scores |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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60 +==========+===========+=========+========+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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61 | C001 | Glycine | 6 | 0.5 |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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62 +----------+-----------+---------+--------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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63 | C002 | Glycine | 3 | 0.34 |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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64 +----------+-----------+---------+--------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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65 | ... | ... | ... | ... |
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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66 +----------+-----------+---------+--------+
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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67 ]]>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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68 </token>
2f9c19fa4346 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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69 </macros>