Mercurial > repos > galaxyp > msconvert
annotate README.md @ 17:ab6c14374bc0 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
| author | galaxyp |
|---|---|
| date | Thu, 15 Aug 2024 16:19:28 +0000 |
| parents | 545054b15d7c |
| children |
| rev | line source |
|---|---|
| 8 | 1 GalaxyP - ProteoWizard msconvert |
| 2 ================================ | |
| 3 | |
|
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
4 * Home: <https://github.com/galaxyproteomics/tools-galaxyp/> |
| 8 | 5 * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert> |
| 6 * Tool ID: `msconvert` | |
| 7 | |
| 0 | 8 |
| 8 | 9 Description |
| 10 ----------- | |
| 0 | 11 |
| 8 | 12 msconvert from ProteoWizard. |
| 13 | |
|
16
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
14 Convert and/or filter mass spectrometry files using the offical Docker container. |
|
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
15 Using the Docker container requires agreeing to each vendor's license (for using their proprietary data access libraries): http://www.proteowizard.org/licenses.html |
|
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
16 |
|
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
17 Main web site: http://www.proteowizard.org |
| 8 | 18 |
| 19 See: | |
| 0 | 20 |
| 8 | 21 * <http://proteowizard.sourceforge.net/> |
| 22 * <http://proteowizard.sourceforge.net/tools/msconvert.html> | |
| 23 | |
| 24 | |
|
16
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
25 #### Note about installing older versions: |
|
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
26 |
|
545054b15d7c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents:
10
diff
changeset
|
27 Version 0.3.0 (2016) and earlier require manual installation of ProteoWizard, and may require a Windows environment. |
| 0 | 28 |
| 8 | 29 Due to potential difficulties installing ProteoWizard with vendor library support, tools for interacting with vendor types are seperated out into their own wrappers. Galaxy is generally deployed under Linux, but vendor support in ProteoWizard requires .NET 4.0. There are at least two ways to get this to work: |
| 30 | |
| 31 * Galaxy jobs may be configured to submit to a Windows host with ProteoWizard installed using the [LWR](https://wiki.g2.bx.psu.edu/Admin/Config/LWR). | |
| 0 | 32 |
| 8 | 33 * ProteoWizard can be installed under Wine. Guidance on how to set this up and package such environments for cloud deployments can be found here: <https://github.com/jmchilton/proteomics-wine-env> |
| 34 | |
| 35 | |
| 36 GalaxyP Community | |
| 37 ----------------- | |
| 0 | 38 |
|
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
39 Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: |
| 8 | 40 |
|
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
41 <https://github.com/galaxyproteomics> |
| 8 | 42 |
| 43 | |
| 44 License | |
| 45 ------- | |
| 0 | 46 |
| 8 | 47 Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. |
| 48 | |
| 49 To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. | |
| 0 | 50 |
| 8 | 51 You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. |
| 52 | |
| 53 You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. | |
| 54 | |
| 0 | 55 |
| 8 | 56 Contributing |
| 57 ------------ | |
| 0 | 58 |
|
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
59 Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> |
| 0 | 60 |
| 61 | |
| 8 | 62 Authors |
| 63 ------- | |
| 64 | |
| 65 Authors and contributors: | |
| 0 | 66 |
| 8 | 67 * Björn Grüning |
| 68 * Cody Wang | |
| 69 * Fred Sadler | |
| 70 * John Chilton <jmchilton@gmail.com> | |
| 71 * Minnesota Supercomputing Institute, Univeristy of Minnesota | |
|
10
9d5de24e6ef7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
9
diff
changeset
|
72 * Jeremy Volkening, University of Wisconsin-Madison |