Mercurial > repos > recetox > matchms_formatter

annotate macros.xml @ 10:1b09315a3f87 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:59 +0000
parents e1ee139b279a
children ae45992f969e
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60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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1 <macros>
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 <token name="@TOOL_VERSION@">0.20.0</token>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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3
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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4 <xml name="creator">
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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5 <creator>
5
f9c4f477ae91 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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60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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7 <person
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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8 givenName="Helge"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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9 familyName="Hecht"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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10 url="https://github.com/hechth"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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11 identifier="0000-0001-6744-996X" />
1
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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12 <person
4
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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13 givenName="Maksym"
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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14 familyName="Skoryk"
966b4134ad12 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"
966b4134ad12 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" />
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17 <person
1
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18 givenName="Zargham"
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19 familyName="Ahmad"
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20 url="https://github.com/zargham-ahmad"
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21 identifier="0000-0002-6096-224X" />
6
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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22 <person
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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23 givenName="Wudmir"
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24 familyName="Rojas"
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25 url="https://github.com/wverastegui"
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26 identifier="0000-0001-7036-9987" />
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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27 <organization
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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28 url="https://www.recetox.muni.cz/"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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30 name="RECETOX MUNI" />
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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31 </creator>
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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32 </xml>
4
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33
10
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34 <xml name="bio.tools">
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35 <xrefs>
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36 <xref type="bio.tools">matchms</xref>
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37 </xrefs>
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38 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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39
10
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40 <xml name="similarity_metrics">
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41 <option value="CosineGreedy" selected="true">CosineGreedy</option>
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42 <option value="CosineHungarian">CosineHungarian</option>
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43 <option value="ModifiedCosine">ModifiedCosine</option>
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44 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
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45 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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46
10
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47 <xml name="similarity_algorithm_params">
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48 <section name="algorithm" title="Algorithm Parameters" expanded="true">
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49 <param label="tolerance [Da]" name="tolerance" type="float" value="0.1"
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50 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
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51 <param label="mz_power" name="mz_power" type="float" value="0.0"
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52 help="The power to raise mz to in the cosine function."/>
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53 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
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54 help="The power to raise intensity to in the cosine function."/>
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55 </section>
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56 </xml>
0
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57
10
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58 <xml name="input_param">
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59 <conditional name="scores">
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60 <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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61 checked="false"/>
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62 <when value="TRUE">
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63 <param label="Scores object" name="scores_in" type="data" format="json"
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64 help="Scores objects calculated previously using one of the matchms similarity tools." />
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65 <param label="join type" name="join_type" type="select" display="radio"
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66 help="The join type to use for appending scores - see [1] for details.">
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67 <option value="left" selected="true">left</option>
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68 <option value="inner">inner</option>
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69 <option value="right">right</option>
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70 <option value="outer">outer</option>
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71 </param>
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72 </when>
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73 <when value="FALSE">
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74 <param label="Queries spectra" name="queries" type="data" format="msp"
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75 help="Query mass spectra to match against references."/>
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76 <param label="Reference spectra" name="references" type="data" format="msp"
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77 help="Reference mass spectra to match against as library."/>
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78 </when>
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79 </conditional>
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80 </xml>
0
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81
10
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82 <xml name="citations">
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83 <citations>
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84 <citation type="doi">10.5281/zenodo.7178586</citation>
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85 <citation type="doi">10.21105/joss.02411</citation>
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86 </citations>
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87 </xml>
5
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88
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89 <token name="@init_scores@">
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90 from matchms.importing import load_from_msp, scores_from_json
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91 from matchms import Scores
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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92 #if $scores.use_scores
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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93 scores = scores_from_json("$scores_in")
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94 join_type = "$scores.join_type"
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95 #else
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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96 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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97 join_type = "left"
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98 #end if
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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99 </token>
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100
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101 <token name="@init_logger@">
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102 from matchms import set_matchms_logger_level
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103 set_matchms_logger_level("WARNING")
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104 </token>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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105 </macros>