Mercurial > repos > recetox > matchms_metadata_export

comparison macros.xml @ 0:dfdbccfa8753 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c10d901c526d0895869d18a1d1bdd1ea58ed7473
author recetox
date Thu, 18 May 2023 14:07:28 +0000
parents
children f04610d25411
comparison
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-1:000000000000 0:dfdbccfa8753
1 <macros>
2 <token name="@TOOL_VERSION@">0.17.0</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 <token name="@HELP_matchms@">
35 <![CDATA[
36 Documentation
37 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
38 and https://matchms.readthedocs.io/en/latest/.
39
40 Upstream Tools
41 +-----------+---------------+--------+-----------+
42 | Name | Output File | Format | Parameter |
43 +===========+===============+========+===========+
44 | RAMClustR | Mass spectra | msp | references|
45 +-----------+---------------+--------+-----------+
46 | RAMClustR | Mass spectra | msp | queries |
47 +-----------+---------------+--------+-----------+
48
49 Downstream Tools
50 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
51 ]]>
52 </token>
53
54 <token name="@HELP_matchms_networking@">
55 <![CDATA[
56 Documentation
57 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
58 and https://matchms.readthedocs.io/en/latest/.
59
60 **Upstream Tools**
61
62 matchMS similarity
63
64 **Downstream Tools**
65
66 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
67 ]]>
68 </token>
69
70 <token name="@HELP_formatter@">
71 <![CDATA[
72 Usage
73 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
74 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
75
76 Input Table Format
77 The tool expects a JSON file containing serialized matchMS Scores object.
78
79 Output Table Format
80 +----------+-----------+---------+--------+
81 | query | reference | matches | scores |
82 +==========+===========+=========+========+
83 | C001 | Glycine | 6 | 0.5 |
84 +----------+-----------+---------+--------+
85 | C002 | Glycine | 3 | 0.34 |
86 +----------+-----------+---------+--------+
87 | ... | ... | ... | ... |
88 +----------+-----------+---------+--------+
89 ]]>
90 </token>
91
92 <xml name="citations">
93 <citations>
94 <citation type="doi">10.5281/zenodo.7178586</citation>
95 <citation type="doi">10.21105/joss.02411</citation>
96 </citations>
97 </xml>
98
99 </macros>