Mercurial > repos > computational-metabolomics > mspurity_frag4feature
annotate README.rst @ 8:cb4aeec93d49 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author | computational-metabolomics |
---|---|
date | Wed, 12 Jun 2024 16:08:23 +0000 |
parents | e9fbb65451f6 |
children | 174a523cb1da |
rev | line source |
---|---|
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
1 msPurity for Galaxy |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
2 ======================== |
8
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
3 |Git| |Bioconda| |License| |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
4 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
5 |
8
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
6 Version v1.16.2+galaxy2 |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
7 ------------------------ |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
8 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
9 - msPurity |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
10 - bioconductor-mspurity v1.16.2 |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
11 - Galaxy tools |
8
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
12 - v2 |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
13 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
14 About |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
15 ------ |
309dcd558030
"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 |
309dcd558030
"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 |
309dcd558030
"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. |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
19 |
309dcd558030
"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. |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
21 |
309dcd558030
"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>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
23 |
309dcd558030
"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: |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
25 |
309dcd558030
"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/ |
309dcd558030
"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 |
309dcd558030
"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 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
29 * Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
30 * Github code: https://github.com/computational-metabolomics/mspurity |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
31 * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
32 * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
33 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
34 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
35 Dependencies |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
36 ------------------ |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
37 Dependencies for these Galaxy tools should be handled by CONDA. |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
38 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
39 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
40 Galaxy |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
41 ------------------ |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
42 `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. |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
43 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
44 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
45 Authors, contributors & contacts |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
46 ------------------------------------- |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
47 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
48 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
49 - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
50 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
51 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
52 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
53 |
7
e9fbb65451f6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents:
6
diff
changeset
|
54 |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
55 Changes |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
56 ------------------------- |
8
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
57 v1.16.2-galaxy2 |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
58 - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
59 - Cleanup of xml based on updated lint requirements |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
60 - Fix combineAnnotation tests |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
61 - Cleanup of repository folders |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
62 - github actions temp update (lintr removed) |
cb4aeec93d49
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
computational-metabolomics
parents:
7
diff
changeset
|
63 |
7
e9fbb65451f6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents:
6
diff
changeset
|
64 v1.16.2-galaxy1 |
e9fbb65451f6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents:
6
diff
changeset
|
65 - Fix for "scan" option for spectral matching |
e9fbb65451f6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents:
6
diff
changeset
|
66 - Add allfrag option for filterFragSpectra |
e9fbb65451f6
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
parents:
6
diff
changeset
|
67 |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
68 v1.16.2-galaxy0 |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
69 - Version bump |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
70 - Fix for intra spectral matching |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
71 - Fix for typo https://github.com/computational-metabolomics/mspurity-galaxy/pull/43 |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
72 - Lint fixes |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
73 |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
74 v1.12.2-galaxy3 |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
75 - Bug fix reference to offsets in conditional #41 |
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
76 |
4
0fe389e3f871
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
3
diff
changeset
|
77 v1.12.2-galaxy2 |
0fe389e3f871
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
3
diff
changeset
|
78 - Bug fix for using custom library sqlite database from Galaxy UI |
0fe389e3f871
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
3
diff
changeset
|
79 - Bug fix for "allfrag" for createDatabase |
0fe389e3f871
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
3
diff
changeset
|
80 |
0fe389e3f871
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
computational-metabolomics
parents:
3
diff
changeset
|
81 |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
82 v1.12.2-galaxy1 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
83 - grpPeaklist reference incorrect in createDatabase.xml |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
84 - Add custom adduct handling for createMSP |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
85 - Change output of flagRemove to tabular |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
86 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
87 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
88 v1.12.2-galaxy0 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
89 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
90 - Optional summary output for combineAnnotations (for very large output) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
91 - Extra column added to flagRemove output |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
92 - Hide probmetab input |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
93 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs" |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
94 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
95 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
96 v1.12.1-galaxy0 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
97 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_ |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
98 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
99 v1.12.0-galaxy1 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
100 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
101 - Exit script without error for flagRemove |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
102 - Username updated in Toolshed yaml |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
103 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
104 v1.12.0-galaxy0 |
6
d4a17be5429a
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
parents:
5
diff
changeset
|
105 - Updates for Bioconductor stable msPurity v1.12.0 release |
3
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
106 - Additional columns added for spectral matching (for msnpy use case) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
107 - Merge of v1.11.4-galaxy1 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
108 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
109 v1.11.4-galaxy1 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
110 - Not submitted to toolshed |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
111 - Update to follow IUC guidelines for Galaxy tool development |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
112 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
113 v1.11.4-galaxy0.2.7 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
114 - submitted to test toolshed (20190927) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
115 - Bug fix for spectralMatching choice of instrument types |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
116 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
117 v1.11.4-galaxy0.2.6: |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
118 - submitted to test toolshed (20190924) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
119 - Bug fix for createAnnotation database local path |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
120 - Update of instrument types for spectral matching |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
121 - Update of split_msp tool to handle different MSP types |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
122 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
123 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
124 v1.11.4-galaxy0.2.5: |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
125 - submitted to test toolshed (20190913) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
126 - Added ppmInterp parameter to purityA |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
127 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
128 - Update of spectralMatching tool to use either sqlite, postgres or mysql database |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
129 - Added include_adducts parameter to createMSP |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
130 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
131 v1.11.3-galaxy0.2.5: |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
132 - Note: This was not pushed to test toolshed |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
133 - Clean up of the versioning to be in line with IUC |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
134 - All tools updated with the same versioning |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
135 - Bump to msPurity v1.11.3 to so EIC is calculated for all features |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
136 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
137 v0.2.5 (spectralMatching): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
138 - spectralMatching - Extra details from matched library spectra is now added to the database (fix) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
139 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
140 v0.2.4 (all tools): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
141 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
142 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
143 v0.2.2 (spectralMatching): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
144 - spectralMatching - Extra details from matched library spectra is now added to the database |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
145 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
146 v0.2.3 (createDatabase): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
147 - createDatabase.xml fix for EIC creation |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
148 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
149 v0.2.2 (createDatabase, flagRemove, combineAnnotation): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
150 - createDatabase.xml fix for xcms3 and CAMERA |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
151 - flagRemove xcms3 fix |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
152 - combineAnnotation Made sirius, probmetab and metfrag optional |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
153 - combineAnnotation fix column sirius |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
154 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
155 v0.2.1 (all tools): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
156 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
157 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
158 v0.2.0 (all tools): |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
159 - Update all tools to be more consistent with msPurity core code |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
160 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
161 License |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
162 ------- |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
163 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_) |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
164 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
165 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
166 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
167 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
168 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
169 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
170 :target: https://github.com/computational-metabolomics/mspurity-galaxy |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
171 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
172 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
173 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
174 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
175 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
176 :target: https://www.gnu.org/licenses/gpl-3.0.html |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
177 |
309dcd558030
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
computational-metabolomics
parents:
diff
changeset
|
178 |