annotate README.rst @ 9:374022b7b469 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:36:53 +0000
parents b16952cc06d2
children 13034c3886f2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
1 msPurity for Galaxy
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
2 ========================
8
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
3 |Git| |Bioconda| |License|
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
4
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
5
9
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
6 Version v1.28.0+galaxy0
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
7 ------------------------
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
8
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
9 - msPurity
9
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
10 - bioconductor-mspurity v1.28.0
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
11 - Galaxy tools
9
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
12 - v0
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
13
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
14 About
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
15 ------
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
16 Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
17 LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
18 anticipated precursor ion purity to guide a later fragmentation experiment.
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
19
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
20 Additional, tools available to perform LC-MS/MS spectral matching.
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
21
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
22 Associated paper `msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics. Analytical Chemistry <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
23
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
24 Use the following links for more details of the msPurity R package:
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
25
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
26 * Bioconductor: http://bioconductor.org/packages/msPurity/
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
27 * Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
28 * Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
29 * Github code: https://github.com/computational-metabolomics/mspurity
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
30 * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
31
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
32
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
33 Dependencies
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
34 ------------------
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
35 Dependencies for these Galaxy tools should be handled by CONDA.
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
36
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
37
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
38 Galaxy
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
39 ------------------
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
40 `Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
41
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
42
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
43 Authors, contributors & contacts
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
44 -------------------------------------
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
45
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
46 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
47 - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
48 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
49 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
50 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
51
7
942e676515fe "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents: 6
diff changeset
52
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
53 Changes
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
54 -------------------------
9
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
55 v1.28.0-galaxy0
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
56 - Version bump to v1.28.0
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
57 - createMSP now uses the median precursor MZ and precursor RT in the MSP files
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
58 - flagRemove updated to handle different xcms version objects internally within msPurity R function
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
59 - Relevant unit tests updated and further tidying up of repo
374022b7b469 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
computational-metabolomics
parents: 8
diff changeset
60
8
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
61 v1.16.2-galaxy2
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
62 - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
63 - Cleanup of xml based on updated lint requirements
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
64 - Fix combineAnnotation tests
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
65 - Cleanup of repository folders
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
66 - github actions temp update (lintr removed)
b16952cc06d2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents: 7
diff changeset
67
7
942e676515fe "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents: 6
diff changeset
68 v1.16.2-galaxy1
942e676515fe "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents: 6
diff changeset
69 - Fix for "scan" option for spectral matching
942e676515fe "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents: 6
diff changeset
70 - Add allfrag option for filterFragSpectra
942e676515fe "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents: 6
diff changeset
71
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
72 v1.16.2-galaxy0
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
73 - Version bump
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
74 - Fix for intra spectral matching
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
75 - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
76 - Lint fixes
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
77
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
78 v1.12.2-galaxy3
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
79 - Bug fix reference to offsets in conditional #41
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
80
4
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 3
diff changeset
81 v1.12.2-galaxy2
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 3
diff changeset
82 - Bug fix for using custom library sqlite database from Galaxy UI
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 3
diff changeset
83 - Bug fix for "allfrag" for createDatabase
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 3
diff changeset
84
7856fc53df1d "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents: 3
diff changeset
85
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
86 v1.12.2-galaxy1
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
87 - grpPeaklist reference incorrect in createDatabase.xml
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
88 - Add custom adduct handling for createMSP
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
89 - Change output of flagRemove to tabular
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
90
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
91
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
92 v1.12.2-galaxy0
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
93 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
94 - Optional summary output for combineAnnotations (for very large output)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
95 - Extra column added to flagRemove output
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
96 - Hide probmetab input
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
97 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
98
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
99
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
100 v1.12.1-galaxy0
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
101 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
102
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
103 v1.12.0-galaxy1
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
104 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
105 - Exit script without error for flagRemove
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
106 - Username updated in Toolshed yaml
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
107
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
108 v1.12.0-galaxy0
6
6b9a83e08467 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents: 5
diff changeset
109 - Updates for Bioconductor stable msPurity v1.12.0 release
3
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
110 - Additional columns added for spectral matching (for msnpy use case)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
111 - Merge of v1.11.4-galaxy1
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
112
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
113 v1.11.4-galaxy1
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
114 - Not submitted to toolshed
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
115 - Update to follow IUC guidelines for Galaxy tool development
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
116
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
117 v1.11.4-galaxy0.2.7
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
118 - submitted to test toolshed (20190927)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
119 - Bug fix for spectralMatching choice of instrument types
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
120
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
121 v1.11.4-galaxy0.2.6:
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
122 - submitted to test toolshed (20190924)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
123 - Bug fix for createAnnotation database local path
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
124 - Update of instrument types for spectral matching
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
125 - Update of split_msp tool to handle different MSP types
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
126
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
127
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
128 v1.11.4-galaxy0.2.5:
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
129 - submitted to test toolshed (20190913)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
130 - Added ppmInterp parameter to purityA
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
131 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
132 - Update of spectralMatching tool to use either sqlite, postgres or mysql database
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
133 - Added include_adducts parameter to createMSP
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
134
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
135 v1.11.3-galaxy0.2.5:
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
136 - Note: This was not pushed to test toolshed
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
137 - Clean up of the versioning to be in line with IUC
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
138 - All tools updated with the same versioning
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
139 - Bump to msPurity v1.11.3 to so EIC is calculated for all features
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
140
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
141 v0.2.5 (spectralMatching):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
142 - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
143
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
144 v0.2.4 (all tools):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
145 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
146
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
147 v0.2.2 (spectralMatching):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
148 - spectralMatching - Extra details from matched library spectra is now added to the database
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
149
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
150 v0.2.3 (createDatabase):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
151 - createDatabase.xml fix for EIC creation
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
152
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
153 v0.2.2 (createDatabase, flagRemove, combineAnnotation):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
154 - createDatabase.xml fix for xcms3 and CAMERA
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
155 - flagRemove xcms3 fix
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
156 - combineAnnotation Made sirius, probmetab and metfrag optional
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
157 - combineAnnotation fix column sirius
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
158
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
159 v0.2.1 (all tools):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
160 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
161
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
162 v0.2.0 (all tools):
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
163 - Update all tools to be more consistent with msPurity core code
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
164
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
165 License
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
166 -------
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
167 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
168
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
169
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
170 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
171 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
172
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
173 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
174 :target: https://github.com/computational-metabolomics/mspurity-galaxy
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
175
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
176 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
177 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
178
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
179 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
180 :target: https://www.gnu.org/licenses/gpl-3.0.html
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
181
1cba235b1972 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff changeset
182