Mercurial > repos > recetox > matchms_filtering
annotate macros.xml @ 3:1f2b13dbc0c8 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
author | recetox |
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date | Tue, 18 Oct 2022 13:22:20 +0000 |
parents | f814052fbdc5 |
children | 357df6c47d92 |
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0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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1 <macros> |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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2 <token name="@TOOL_VERSION@">0.17.0</token> |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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3 |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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4 <xml name="creator"> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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5 <creator> |
3
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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6 <yield/> |
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3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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7 <person |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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8 givenName="Helge" |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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9 familyName="Hecht" |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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10 url="https://github.com/hechth" |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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11 identifier="0000-0001-6744-996X" /> |
1
b8e9a7c7add2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
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12 <person |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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13 givenName="Maksym" |
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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14 familyName="Skoryk" |
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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15 url="https://github.com/maximskorik" |
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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16 identifier="0000-0003-2056-8018" /> |
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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17 <person |
1
b8e9a7c7add2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
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18 givenName="Zargham" |
b8e9a7c7add2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
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19 familyName="Ahmad" |
b8e9a7c7add2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents:
0
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20 url="https://github.com/zargham-ahmad" |
b8e9a7c7add2
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
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21 identifier="0000-0002-6096-224X" /> |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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22 <organization |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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23 url="https://www.recetox.muni.cz/" |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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24 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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25 name="RECETOX MUNI" /> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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26 </creator> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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27 </xml> |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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28 |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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29 <token name="@HELP_matchms@"> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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30 <![CDATA[ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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31 Documentation |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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32 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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33 and https://matchms.readthedocs.io/en/latest/. |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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34 |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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35 Upstream Tools |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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36 +-----------+---------------+--------+-----------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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37 | Name | Output File | Format | Parameter | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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38 +===========+===============+========+===========+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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39 | RAMClustR | Mass spectra | msp | references| |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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40 +-----------+---------------+--------+-----------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff
changeset
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41 | RAMClustR | Mass spectra | msp | queries | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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42 +-----------+---------------+--------+-----------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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43 |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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44 Downstream Tools |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents:
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45 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**. |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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46 ]]> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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47 </token> |
3
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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48 |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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49 <token name="@HELP_matchms_networking@"> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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50 <![CDATA[ |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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51 Documentation |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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52 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
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53 and https://matchms.readthedocs.io/en/latest/. |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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54 |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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55 **Upstream Tools** |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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56 |
3
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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57 matchMS similarity |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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58 |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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59 **Downstream Tools** |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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60 |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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61 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape). |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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62 ]]> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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63 </token> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
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64 |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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65 <token name="@HELP_formatter@"> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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66 <![CDATA[ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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67 Usage |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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68 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**. |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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69 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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70 |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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71 Input Table Format |
2
f814052fbdc5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
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72 The tool expects a JSON file containing serialized matchMS Scores object. |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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73 |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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74 Output Table Format |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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75 +----------+-----------+---------+--------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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76 | query | reference | matches | scores | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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77 +==========+===========+=========+========+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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78 | C001 | Glycine | 6 | 0.5 | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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79 +----------+-----------+---------+--------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
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80 | C002 | Glycine | 3 | 0.34 | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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81 +----------+-----------+---------+--------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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82 | ... | ... | ... | ... | |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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83 +----------+-----------+---------+--------+ |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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84 ]]> |
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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85 </token> |
3
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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86 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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87 <xml name="citations"> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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88 <citations> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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89 <citation type="doi">10.5281/zenodo.7178586</citation> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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90 <citation type="doi">10.21105/joss.02411</citation> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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91 </citations> |
1f2b13dbc0c8
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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92 </xml> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
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93 |
0
3d275fbdf741
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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94 </macros> |