comparison macros.xml @ 0:84af792d3a78 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:27:04 +0000
parents
children df85b26201d1
comparison
equal deleted inserted replaced
-1:000000000000 0:84af792d3a78
1 <macros>
2 <token name="@TOOL_VERSION@">0.20.0</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="boolean" truevalue="TRUE" falsevalue="FALSE"
61 checked="false"/>
62 <when value="TRUE">
63 <param label="Scores object" name="scores_in" type="data" format="json"
64 help="Scores objects calculated previously using one of the matchms similarity tools." />
65 <param label="join type" name="join_type" type="select" display="radio"
66 help="The join type to use for appending scores - see [1] for details.">
67 <option value="left" selected="true">left</option>
68 <option value="inner">inner</option>
69 <option value="right">right</option>
70 <option value="outer">outer</option>
71 </param>
72 </when>
73 <when value="FALSE">
74 <param label="Queries spectra" name="queries" type="data" format="msp"
75 help="Query mass spectra to match against references."/>
76 <param label="Reference spectra" name="references" type="data" format="msp"
77 help="Reference mass spectra to match against as library."/>
78 </when>
79 </conditional>
80 </xml>
81
82 <xml name="citations">
83 <citations>
84 <citation type="doi">10.5281/zenodo.7178586</citation>
85 <citation type="doi">10.21105/joss.02411</citation>
86 </citations>
87 </xml>
88
89 <token name="@init_scores@">
90 from matchms.importing import load_from_msp, scores_from_json
91 from matchms import Scores
92 #if $scores.use_scores
93 scores = scores_from_json("$scores_in")
94 join_type = "$scores.join_type"
95 #else
96 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
97 join_type = "left"
98 #end if
99 </token>
100
101 <token name="@init_logger@">
102 from matchms import set_matchms_logger_level
103 set_matchms_logger_level("WARNING")
104 </token>
105 </macros>