Mercurial > repos > recetox > matchms_formatter

annotate macros.xml @ 29:6501d0287dcd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4
author recetox
date Tue, 04 Jun 2024 07:13:22 +0000
parents 8bd942dcf1ad
children 9e3c83d2afc3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
1 <macros>
28
8bd942dcf1ad planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
recetox
parents: 14
diff changeset
2 <token name="@TOOL_VERSION@">0.25.0</token>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
3
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
4 <xml name="creator">
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
5 <creator>
5
f9c4f477ae91 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents: 4
diff changeset
6 <yield/>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
7 <person
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
8 givenName="Helge"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
9 familyName="Hecht"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
10 url="https://github.com/hechth"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
11 identifier="0000-0001-6744-996X" />
1
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents: 0
diff changeset
12 <person
4
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
13 givenName="Maksym"
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
14 familyName="Skoryk"
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
15 url="https://github.com/maximskorik"
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
16 identifier="0000-0003-2056-8018" />
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
17 <person
1
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents: 0
diff changeset
18 givenName="Zargham"
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents: 0
diff changeset
19 familyName="Ahmad"
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents: 0
diff changeset
20 url="https://github.com/zargham-ahmad"
28a252f3b682 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
recetox
parents: 0
diff changeset
21 identifier="0000-0002-6096-224X" />
6
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
parents: 5
diff changeset
22 <person
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
parents: 5
diff changeset
23 givenName="Wudmir"
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
parents: 5
diff changeset
24 familyName="Rojas"
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
parents: 5
diff changeset
25 url="https://github.com/wverastegui"
e1ee139b279a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
recetox
parents: 5
diff changeset
26 identifier="0000-0001-7036-9987" />
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
27 <organization
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
28 url="https://www.recetox.muni.cz/"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
30 name="RECETOX MUNI" />
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
31 </creator>
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
32 </xml>
4
966b4134ad12 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
recetox
parents: 1
diff changeset
33
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
34 <xml name="bio.tools">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
35 <xrefs>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
36 <xref type="bio.tools">matchms</xref>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
37 </xrefs>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
38 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
39
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
40 <xml name="similarity_metrics">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
41 <option value="CosineGreedy" selected="true">CosineGreedy</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
42 <option value="CosineHungarian">CosineHungarian</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
43 <option value="ModifiedCosine">ModifiedCosine</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
44 <option value="NeutralLossesCosine">NeutralLossesCosine</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
45 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
46
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
47 <xml name="similarity_algorithm_params">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
48 <section name="algorithm" title="Algorithm Parameters" expanded="true">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
49 <param label="tolerance [Da]" name="tolerance" type="float" value="0.1"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
50 help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
51 <param label="mz_power" name="mz_power" type="float" value="0.0"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
52 help="The power to raise mz to in the cosine function."/>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
53 <param label="intensity_power" name="intensity_power" type="float" value="1.0"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
54 help="The power to raise intensity to in the cosine function."/>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
55 </section>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
56 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
57
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
58 <xml name="input_param">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
59 <conditional name="scores">
11
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
60 <param name="use_scores" label="Use Scores Object" type="select">
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
61 <option value="False" selected="true">FALSE</option>
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
62 <option value="True">TRUE</option>
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
63 </param>
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
64 <when value="True">
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
65 <param label="Scores object" name="scores_in" type="data" format="json"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
66 help="Scores objects calculated previously using one of the matchms similarity tools." />
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
67 <param label="join type" name="join_type" type="select" display="radio"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
68 help="The join type to use for appending scores - see [1] for details.">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
69 <option value="left" selected="true">left</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
70 <option value="inner">inner</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
71 <option value="right">right</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
72 <option value="outer">outer</option>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
73 </param>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
74 </when>
11
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
75 <when value="False">
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
76 <param label="Queries spectra" name="queries" type="data" format="msp"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
77 help="Query mass spectra to match against references."/>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
78 <param label="Reference spectra" name="references" type="data" format="msp"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
79 help="Reference mass spectra to match against as library."/>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
80 </when>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
81 </conditional>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
82 </xml>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
83
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
84 <xml name="citations">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
85 <citations>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
86 <citation type="doi">10.5281/zenodo.7178586</citation>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
87 <citation type="doi">10.21105/joss.02411</citation>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
88 </citations>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
89 </xml>
5
f9c4f477ae91 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents: 4
diff changeset
90
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
91 <token name="@init_scores@">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
92 from matchms.importing import load_from_msp, scores_from_json
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
93 from matchms import Scores
11
ae45992f969e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 10
diff changeset
94 #if $scores.use_scores == "True"
10
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
95 scores = scores_from_json("$scores_in")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
96 join_type = "$scores.join_type"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
97 #else
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
98 scores = Scores(references=list(load_from_msp("$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
recetox
parents: 6
diff changeset
99 join_type = "left"
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
100 #end if
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
101 </token>
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
102
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
103 <token name="@init_logger@">
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
104 from matchms import set_matchms_logger_level
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
105 set_matchms_logger_level("WARNING")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 6
diff changeset
106 </token>
0
60f34912b3de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
107 </macros>