Mercurial > repos > recetox > spec2vec_similarity

comparison macros.xml @ 0:721a4e666191 draft default tip

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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 14:30:10 +0000
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-1:000000000000 0:721a4e666191
1 <macros>
2 <token name="@TOOL_VERSION@">0.8.0</token>
3
4 <xml name="creator">
5 <creator>
6 <person
7 givenName="Maksym"
8 familyName="Skoryk"
9 url="https://github.com/maximskorik"
10 identifier="0000-0003-2056-8018" />
11 <person
12 givenName="Helge"
13 familyName="Hecht"
14 url="https://github.com/hechth"
15 identifier="0000-0001-6744-996X" />
16 <organization
17 url="https://www.recetox.muni.cz/"
18 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
19 name="RECETOX MUNI" />
20 </creator>
21 </xml>
22
23 <xml name="edam">
24 <xrefs>
25 <xref type="bio.tools">spec2vec</xref>
26 </xrefs>
27 </xml>
28
29 <xml name="input_param">
30 <conditional name="scores">
31 <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
32 checked="false"/>
33 <when value="TRUE">
34 <param label="Scores object" name="scores_in" type="data" format="json"
35 help="Scores objects calculated previously using one of the matchms similarity tools." />
36 </when>
37 <when value="FALSE">
38 <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
39 help="Query mass spectra to match against references."/>
40 <param label="Reference spectra" name="references" type="data" format="msp,mgf"
41 help="Reference mass spectra to match against as library."/>
42 </when>
43 </conditional>
44 </xml>
45
46 <xml name="citations">
47 <citations>
48 <citation type="doi">10.1371/journal.pcbi.1008724</citation>
49 </citations>
50 </xml>
51
52 <token name="@init_scores@">
53 from matchms.importing import load_from_msp, scores_from_json
54 from matchms import Scores
55 #if $scores.use_scores
56 scores = scores_from_json("$scores_in")
57 #else
58 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
59 #end if
60 </token>
61
62 <token name="@init_logger@">
63 from matchms import set_matchms_logger_level
64 set_matchms_logger_level("WARNING")
65 </token>
66
67 <token name="@init_model@">
68 import json
69 from spec2vec.serialization.model_importing import load_weights, Word2VecLight
70
71 with open("${model_metadata}", "r", encoding="utf-8") as f:
72 model: dict = json.load(f)
73 del (model["mapfile_path"])
74
75 weights = load_weights("${model_weights}", model["__weights_format"])
76 model = Word2VecLight(model, weights)
77 </token>
78 </macros>