Mercurial > repos > recetox > matchms_formatter

comparison macros.xml @ 0:60f34912b3de draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author recetox
date Tue, 22 Mar 2022 16:08:45 +0000
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children 28a252f3b682
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-1:000000000000 0:60f34912b3de
1 <macros>
2 <token name="@TOOL_VERSION@">0.14.0</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>