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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:22:23 +0000
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1 <macros>
2 <token name="@HELP_matchms@">
3 Documentation
4 The Python library matchms provides functions to convert, filter and compare mass spectrometry data.
5 For an overview of the different galaxy modules, see the figure below.
6 For detailed documentation on the tool, see https://github.com/matchms/matchms/blob/master/README.rst
7 and https://matchms.readthedocs.io/en/latest/ for the Python API.
8
9 To get more familiar with the library, there is a `tutorial`_ available which explains how to build a mass spectrometry data processing
10 pipeline with matchms.
11
12 .. _tutorial: https://medium.com/escience-center/build-your-own-mass-spectrometry-analysis-pipeline-in-python-using-matchms-part-i-d96c718c68ee
13
14 Overview
15 .. image:: https://github.com/RECETOX/galaxytools/raw/29e54e69dab6ab1263f56d35ea19f5d7f284d728/tools/matchms/images/matchms_galaxytools.png
16 :width: 3120
17 :height: 1686
18 :scale: 30
19 :alt: Overview of different matchms galaxytools and how they are connected.
20 </token>
21 <token name="@HELP_matchms_networking@">
22 <![CDATA[
23 Documentation
24 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst
25 and https://matchms.readthedocs.io/en/latest/.
26
27 **Upstream Tools**
28
29 matchms similarity
30
31 **Downstream Tools**
32
33 The output is a network-graph file that can be visualized using graph visualization software (e.g., Cytoscape).
34 ]]>
35 </token>
36
37 <token name="@HELP_formatter@">
38 <![CDATA[
39 Usage
40 This tool creates user friendly tables from the similarity scores produced by **matchms similarity**.
41 The tool can be operated on two modes based on (i) thresholds or (ii) top k matches.
42
43 Input Table Format
44 The tool expects a JSON file containing serialized matchms Scores object.
45
46 Output Table Format
47 +----------+-----------+---------+--------+
48 | query | reference | matches | scores |
49 +==========+===========+=========+========+
50 | C001 | Glycine | 6 | 0.5 |
51 +----------+-----------+---------+--------+
52 | C002 | Glycine | 3 | 0.34 |
53 +----------+-----------+---------+--------+
54 | ... | ... | ... | ... |
55 +----------+-----------+---------+--------+
56 ]]>
57 </token>
58 </macros>