Mercurial > repos > recetox > matchms_networking

comparison macros.xml @ 0:e4ec3592507f draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
author recetox
date Tue, 18 Oct 2022 13:23:28 +0000
parents
children 0009acc67c12
comparison
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-1:000000000000 0:e4ec3592507f
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 <organization
23 url="https://www.recetox.muni.cz/"
24 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
25 name="RECETOX MUNI" />
26 </creator>
27 </xml>
28
29 <token name="@HELP_matchms@">
30 <![CDATA[
31 Documentation
32 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
33 and https://matchms.readthedocs.io/en/latest/.
34
35 Upstream Tools
36 +-----------+---------------+--------+-----------+
37 | Name | Output File | Format | Parameter |
38 +===========+===============+========+===========+
39 | RAMClustR | Mass spectra | msp | references|
40 +-----------+---------------+--------+-----------+
41 | RAMClustR | Mass spectra | msp | queries |
42 +-----------+---------------+--------+-----------+
43
44 Downstream Tools
45 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
46 ]]>
47 </token>
48
49 <token name="@HELP_matchms_networking@">
50 <![CDATA[
51 Documentation
52 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
53 and https://matchms.readthedocs.io/en/latest/.
54
55 **Upstream Tools**
56
57 matchMS similarity
58
59 **Downstream Tools**
60
61 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
62 ]]>
63 </token>
64
65 <token name="@HELP_formatter@">
66 <![CDATA[
67 Usage
68 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
69 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
70
71 Input Table Format
72 The tool expects a JSON file containing serialized matchMS Scores object.
73
74 Output Table Format
75 +----------+-----------+---------+--------+
76 | query | reference | matches | scores |
77 +==========+===========+=========+========+
78 | C001 | Glycine | 6 | 0.5 |
79 +----------+-----------+---------+--------+
80 | C002 | Glycine | 3 | 0.34 |
81 +----------+-----------+---------+--------+
82 | ... | ... | ... | ... |
83 +----------+-----------+---------+--------+
84 ]]>
85 </token>
86
87 <xml name="citations">
88 <citations>
89 <citation type="doi">10.5281/zenodo.7178586</citation>
90 <citation type="doi">10.21105/joss.02411</citation>
91 </citations>
92 </xml>
93
94 </macros>