Mercurial > repos > recetox > matchms_networking

annotate macros.xml @ 0:e4ec3592507f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
1 <macros>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
2 <token name="@TOOL_VERSION@">0.17.0</token>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
3
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
4 <xml name="creator">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
5 <creator>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
6 <yield/>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
7 <person
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
8 givenName="Helge"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
9 familyName="Hecht"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
10 url="https://github.com/hechth"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
11 identifier="0000-0001-6744-996X" />
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
12 <person
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
13 givenName="Maksym"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
14 familyName="Skoryk"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
15 url="https://github.com/maximskorik"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
16 identifier="0000-0003-2056-8018" />
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
17 <person
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
18 givenName="Zargham"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
19 familyName="Ahmad"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
20 url="https://github.com/zargham-ahmad"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
21 identifier="0000-0002-6096-224X" />
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
22 <organization
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
23 url="https://www.recetox.muni.cz/"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
24 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
25 name="RECETOX MUNI" />
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
26 </creator>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
27 </xml>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
28
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
29 <token name="@HELP_matchms@">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
30 <![CDATA[
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
31 Documentation
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
32 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
33 and https://matchms.readthedocs.io/en/latest/.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
34
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
35 Upstream Tools
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
36 +-----------+---------------+--------+-----------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
37 | Name | Output File | Format | Parameter |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
38 +===========+===============+========+===========+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
39 | RAMClustR | Mass spectra | msp | references|
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
40 +-----------+---------------+--------+-----------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
41 | RAMClustR | Mass spectra | msp | queries |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
42 +-----------+---------------+--------+-----------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
43
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
44 Downstream Tools
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
45 The output is a JSON file containing serialized matchMS Scores object. The file can be processed by **matchMS output formatter**.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
46 ]]>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
47 </token>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
48
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
49 <token name="@HELP_matchms_networking@">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
50 <![CDATA[
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
51 Documentation
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
52 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
53 and https://matchms.readthedocs.io/en/latest/.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
54
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
55 **Upstream Tools**
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
56
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
57 matchMS similarity
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
58
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
59 **Downstream Tools**
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
60
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
61 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
62 ]]>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
63 </token>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
64
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
65 <token name="@HELP_formatter@">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
66 <![CDATA[
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
67 Usage
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
68 This tool creates user friendly tables from the similarity scores produced by **matchMS similarity**.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
69 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
70
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
71 Input Table Format
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
72 The tool expects a JSON file containing serialized matchMS Scores object.
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
73
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
74 Output Table Format
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
75 +----------+-----------+---------+--------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
76 | query | reference | matches | scores |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
77 +==========+===========+=========+========+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
78 | C001 | Glycine | 6 | 0.5 |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
79 +----------+-----------+---------+--------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
80 | C002 | Glycine | 3 | 0.34 |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
81 +----------+-----------+---------+--------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
82 | ... | ... | ... | ... |
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
83 +----------+-----------+---------+--------+
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
84 ]]>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
85 </token>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
86
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
87 <xml name="citations">
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
88 <citations>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
89 <citation type="doi">10.5281/zenodo.7178586</citation>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
90 <citation type="doi">10.21105/joss.02411</citation>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
91 </citations>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
92 </xml>
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
93
e4ec3592507f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents:
diff changeset
94 </macros>