Mercurial > repos > recetox > matchms_formatter

comparison macros.xml @ 4:966b4134ad12 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
author recetox
date Tue, 18 Oct 2022 11:02:18 +0000
parents 28a252f3b682
children f9c4f477ae91
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3:574c6331e9db 4:966b4134ad12
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.15.0</token> 2 <token name="@TOOL_VERSION@">0.17.0</token>
3 3
4 <xml name="creator"> 4 <xml name="creator">
5 <creator> 5 <creator>
6 <person 6 <person
7 givenName="Helge" 7 givenName="Helge"
8 familyName="Hecht" 8 familyName="Hecht"
9 url="https://github.com/hechth" 9 url="https://github.com/hechth"
10 identifier="0000-0001-6744-996X" /> 10 identifier="0000-0001-6744-996X" />
11 <person
12 givenName="Maksym"
13 familyName="Skoryk"
14 url="https://github.com/maximskorik"
15 identifier="0000-0003-2056-8018" />
11 <person 16 <person
12 givenName="Zargham" 17 givenName="Zargham"
13 familyName="Ahmad" 18 familyName="Ahmad"
14 url="https://github.com/zargham-ahmad" 19 url="https://github.com/zargham-ahmad"
15 identifier="0000-0002-6096-224X" /> 20 identifier="0000-0002-6096-224X" />
17 url="https://www.recetox.muni.cz/" 22 url="https://www.recetox.muni.cz/"
18 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" 23 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
19 name="RECETOX MUNI" /> 24 name="RECETOX MUNI" />
20 </creator> 25 </creator>
21 </xml> 26 </xml>
22 27
23 <token name="@HELP_matchms@"> 28 <token name="@HELP_matchms@">
24 <![CDATA[ 29 <![CDATA[
25 Documentation 30 Documentation
26 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst 31 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
27 and https://matchms.readthedocs.io/en/latest/. 32 and https://matchms.readthedocs.io/en/latest/.
34 +-----------+---------------+--------+-----------+ 39 +-----------+---------------+--------+-----------+
35 | RAMClustR | Mass spectra | msp | queries | 40 | RAMClustR | Mass spectra | msp | queries |
36 +-----------+---------------+--------+-----------+ 41 +-----------+---------------+--------+-----------+
37 42
38 Downstream Tools 43 Downstream Tools
39 The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks. 44 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
40 ]]> 45 ]]>
41 </token> 46 </token>
42 47
43 <token name="@HELP_formatter@"> 48 <token name="@HELP_formatter@">
44 <![CDATA[ 49 <![CDATA[
45 Usage 50 Usage
46 This tool creates user friendly tables from the data matrices produces by matchms. 51 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
47 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. 52 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
48 53
49 Input Table Format 54 Input Table Format
50 The tool expects two data matrices with the format as depicted below. 55 The tool expects a JSON file containing serialized matchMS Scores object.
51 The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
52
53 +----------+------+------+-----+
54 | | C001 | C002 | ... |
55 +==========+======+======+=====+
56 | Perylene | 0.1 | 0.0 | ... |
57 +----------+------+------+-----+
58 | Glycine | 0.5 | 0.34 | ... |
59 +----------+------+------+-----+
60 | ... | ... | ... | ... |
61 +----------+------+------+-----+
62 56
63 Output Table Format 57 Output Table Format
64 +----------+-----------+---------+--------+ 58 +----------+-----------+---------+--------+
65 | query | reference | matches | scores | 59 | query | reference | matches | scores |
66 +==========+===========+=========+========+ 60 +==========+===========+=========+========+