Mercurial > repos > recetox > spec2vec_similarity

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:23:58 +0000
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881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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1 <macros>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 <token name="@TOOL_VERSION@">0.8.0</token>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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3
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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4 <xml name="creator">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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5 <creator>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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6 <person
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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7 givenName="Maksym"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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8 familyName="Skoryk"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 url="https://github.com/maximskorik"
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10 identifier="0000-0003-2056-8018" />
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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11 <person
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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12 givenName="Helge"
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13 familyName="Hecht"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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14 url="https://github.com/hechth"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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15 identifier="0000-0001-6744-996X" />
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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16 <organization
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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17 url="https://www.recetox.muni.cz/"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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18 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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19 name="RECETOX MUNI" />
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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20 </creator>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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21 </xml>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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22
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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23 <xml name="edam">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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24 <xrefs>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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25 <xref type="bio.tools">spec2vec</xref>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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26 </xrefs>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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27 </xml>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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28
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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29 <xml name="input_param">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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30 <conditional name="scores">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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31 <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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32 checked="false"/>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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33 <when value="TRUE">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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34 <param label="Scores object" name="scores_in" type="data" format="json"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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35 help="Scores objects calculated previously using one of the matchms similarity tools." />
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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36 </when>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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37 <when value="FALSE">
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38 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
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39 help="Query mass spectra to match against references."/>
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40 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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41 help="Reference mass spectra to match against as library."/>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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42 </when>
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43 </conditional>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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44 </xml>
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45
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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46 <xml name="citations">
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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47 <citations>
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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48 <citation type="doi">10.1371/journal.pcbi.1008724</citation>
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49 </citations>
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50 </xml>
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51
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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52 <token name="@init_scores@">
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53 from matchms.importing import load_from_msp, scores_from_json
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54 from matchms import Scores
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55 #if $scores.use_scores
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56 scores = scores_from_json("$scores_in")
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57 #else
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58 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
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59 #end if
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60 </token>
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61
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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62 <token name="@init_logger@">
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63 from matchms import set_matchms_logger_level
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64 set_matchms_logger_level("WARNING")
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65 </token>
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66
881742fff7ff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec commit f79a5b51599254817727bc9028b9797ea994cb4e
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67 <token name="@init_model@">
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68 import json
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69 from spec2vec.serialization.model_importing import load_weights, Word2VecLight
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70
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71 with open("${model_metadata}", "r", encoding="utf-8") as f:
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72 model: dict = json.load(f)
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73 del (model["mapfile_path"])
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74
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75 weights = load_weights("${model_weights}", model["__weights_format"])
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76 model = Word2VecLight(model, weights)
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77 </token>
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78 </macros>