Mercurial > repos > recetox > matchms_filtering

comparison macros.xml @ 1:2f9c19fa4346 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:22:45 +0000
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children b8bf66da7e6f
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0:6303b43e29cb 1:2f9c19fa4346
1 <macros>
2 <token name="@TOOL_VERSION@">0.11.0</token>
3
4 <xml name="creator">
5 <creator>
6 <person
7 givenName="Helge"
8 familyName="Hecht"
9 url="https://github.com/hechth"
10 identifier="0000-0001-6744-996X" />
11 <organization
12 url="https://www.recetox.muni.cz/"
13 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
14 name="RECETOX MUNI" />
15 </creator>
16 </xml>
17
18 <token name="@HELP_matchms@">
19 <![CDATA[
20 Documentation
21 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
22 and https://matchms.readthedocs.io/en/latest/.
23
24 Upstream Tools
25 +-----------+---------------+--------+-----------+
26 | Name | Output File | Format | Parameter |
27 +===========+===============+========+===========+
28 | RAMClustR | Mass spectra | msp | references|
29 +-----------+---------------+--------+-----------+
30 | RAMClustR | Mass spectra | msp | queries |
31 +-----------+---------------+--------+-----------+
32
33 Downstream Tools
34 The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks.
35 ]]>
36 </token>
37
38 <token name="@HELP_formatter@">
39 <![CDATA[
40 Usage
41 This tool creates user friendly tables from the data matrices produces by matchms.
42 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
43
44 Input Table Format
45 The tool expects two data matrices with the format as depicted below.
46 The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms).
47
48 +----------+------+------+-----+
49 | | C001 | C002 | ... |
50 +==========+======+======+=====+
51 | Perylene | 0.1 | 0.0 | ... |
52 +----------+------+------+-----+
53 | Glycine | 0.5 | 0.34 | ... |
54 +----------+------+------+-----+
55 | ... | ... | ... | ... |
56 +----------+------+------+-----+
57
58 Output Table Format
59 +----------+-----------+---------+--------+
60 | query | reference | matches | scores |
61 +==========+===========+=========+========+
62 | C001 | Glycine | 6 | 0.5 |
63 +----------+-----------+---------+--------+
64 | C002 | Glycine | 3 | 0.34 |
65 +----------+-----------+---------+--------+
66 | ... | ... | ... | ... |
67 +----------+-----------+---------+--------+
68 ]]>
69 </token>
70 </macros>