Mercurial > repos > recetox > matchms_remove_spectra
comparison macros.xml @ 0:80df426e7e47 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
author | recetox |
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date | Thu, 30 May 2024 18:07:29 +0000 |
parents | |
children | fbe335d27d25 |
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-1:000000000000 | 0:80df426e7e47 |
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1 <macros> | |
2 <token name="@TOOL_VERSION@">0.25.0</token> | |
3 | |
4 <xml name="creator"> | |
5 <creator> | |
6 <yield/> | |
7 <person | |
8 givenName="Helge" | |
9 familyName="Hecht" | |
10 url="https://github.com/hechth" | |
11 identifier="0000-0001-6744-996X" /> | |
12 <person | |
13 givenName="Maksym" | |
14 familyName="Skoryk" | |
15 url="https://github.com/maximskorik" | |
16 identifier="0000-0003-2056-8018" /> | |
17 <person | |
18 givenName="Zargham" | |
19 familyName="Ahmad" | |
20 url="https://github.com/zargham-ahmad" | |
21 identifier="0000-0002-6096-224X" /> | |
22 <person | |
23 givenName="Wudmir" | |
24 familyName="Rojas" | |
25 url="https://github.com/wverastegui" | |
26 identifier="0000-0001-7036-9987" /> | |
27 <organization | |
28 url="https://www.recetox.muni.cz/" | |
29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" | |
30 name="RECETOX MUNI" /> | |
31 </creator> | |
32 </xml> | |
33 | |
34 <xml name="bio.tools"> | |
35 <xrefs> | |
36 <xref type="bio.tools">matchms</xref> | |
37 </xrefs> | |
38 </xml> | |
39 | |
40 <xml name="similarity_metrics"> | |
41 <option value="CosineGreedy" selected="true">CosineGreedy</option> | |
42 <option value="CosineHungarian">CosineHungarian</option> | |
43 <option value="ModifiedCosine">ModifiedCosine</option> | |
44 <option value="NeutralLossesCosine">NeutralLossesCosine</option> | |
45 </xml> | |
46 | |
47 <xml name="similarity_algorithm_params"> | |
48 <section name="algorithm" title="Algorithm Parameters" expanded="true"> | |
49 <param label="tolerance [Da]" name="tolerance" type="float" value="0.1" | |
50 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/> | |
51 <param label="mz_power" name="mz_power" type="float" value="0.0" | |
52 help="The power to raise mz to in the cosine function."/> | |
53 <param label="intensity_power" name="intensity_power" type="float" value="1.0" | |
54 help="The power to raise intensity to in the cosine function."/> | |
55 </section> | |
56 </xml> | |
57 | |
58 <xml name="input_param"> | |
59 <conditional name="scores"> | |
60 <param name="use_scores" label="Use Scores Object" type="select"> | |
61 <option value="False" selected="true">FALSE</option> | |
62 <option value="True">TRUE</option> | |
63 </param> | |
64 <when value="True"> | |
65 <param label="Scores object" name="scores_in" type="data" format="json" | |
66 help="Scores objects calculated previously using one of the matchms similarity tools." /> | |
67 <param label="join type" name="join_type" type="select" display="radio" | |
68 help="The join type to use for appending scores - see [1] for details."> | |
69 <option value="left" selected="true">left</option> | |
70 <option value="inner">inner</option> | |
71 <option value="right">right</option> | |
72 <option value="outer">outer</option> | |
73 </param> | |
74 </when> | |
75 <when value="False"> | |
76 <param label="Queries spectra" name="queries" type="data" format="msp" | |
77 help="Query mass spectra to match against references."/> | |
78 <param label="Reference spectra" name="references" type="data" format="msp" | |
79 help="Reference mass spectra to match against as library."/> | |
80 </when> | |
81 </conditional> | |
82 </xml> | |
83 | |
84 <xml name="citations"> | |
85 <citations> | |
86 <citation type="doi">10.5281/zenodo.7178586</citation> | |
87 <citation type="doi">10.21105/joss.02411</citation> | |
88 </citations> | |
89 </xml> | |
90 | |
91 <token name="@init_scores@"> | |
92 from matchms.importing import load_from_msp, scores_from_json | |
93 from matchms import Scores | |
94 #if $scores.use_scores == "True" | |
95 scores = scores_from_json("$scores_in") | |
96 join_type = "$scores.join_type" | |
97 #else | |
98 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False) | |
99 join_type = "left" | |
100 #end if | |
101 </token> | |
102 | |
103 <token name="@init_logger@"> | |
104 from matchms import set_matchms_logger_level | |
105 set_matchms_logger_level("WARNING") | |
106 </token> | |
107 </macros> |