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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 05:01:05 -0400
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0:d4b6c9eae635 1:8bac3cc5c5de
1 Tool wrapper for MaxQuant. 1 GalaxyP - MaxQuant
2 ==================
2 3
3 MaxQuant is a Windows only program and so you will likely need to 4 * Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
4 deploy this tool to run on a remote Windows system via the LWR 5 * Tool ID: `maxquant`
5 (https://lwr.readthedocs.org). 6 * Tool Type: `default`
6 7
7 The sample mods file maxquant_mods.loc.sample corresponds to the
8 default modifications MaxQuant is configured with. The Galaxy-P
9 project uses a MaxQuant that has been extended with all of Unimod. To
10 modify MaxQuant in this fashion replace MaxQuant's modifications.xml
11 file with the extended_modifications.xml distributed with this tool
12 and configure Galaxy with the maxquant_mods.loc.sample.extended loc
13 file.# Obtaining Tools
14 8
15 Repositories for all Galaxy-P tools can be found at 9 Description
16 https:/bitbucket.org/galaxyp/. 10 -----------
17 11
18 # Contact 12 Wrapper for the MaxQuant version available in conda.
19 13
20 Please send suggestions for improvements and bug reports to
21 jmchilton@gmail.com.
22 14
23 # License 15 Updating
16 --------
24 17
25 All Galaxy-P tools are licensed under the Apache License Version 2.0 18 MaxQuant often changes the layout of its parameters file.
26 unless otherwise documented. 19 So changes to the code are likely to be necessary when
20 updating to a new version of MaxQuant. The init.py script
21 can be used to initialize the tool with a new list of
22 modifications or enzymes. From the tool dir run:
27 23
28 # Tool Versioning 24 ./init.py -m MODIFICATIONS.XML -e ENZYMES.XML
29 25
30 Galaxy-P tools will have versions of the form X.Y.Z. Versions 26 The location of these xml files usually is:
31 differing only after the second decimal should be completely 27 ANACONDA_DIR/bin/conf/
32 compatible with each other. Breaking changes should result in an
33 increment of the number before and/or after the first decimal. All
34 tools of version less than 1.0.0 should be considered beta.