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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6

GalaxyP - ProteoWizard msconvert
================================

* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert>
* Tool ID: `msconvert`


Description
-----------

msconvert from ProteoWizard.

Convert and/or filter mass spectrometry files using the offical Docker container.
Using the Docker container requires agreeing to each vendor's license (for using their proprietary data access libraries): http://www.proteowizard.org/licenses.html

Main web site: http://www.proteowizard.org

See:

* <http://proteowizard.sourceforge.net/>
* <http://proteowizard.sourceforge.net/tools/msconvert.html>


#### Note about installing older versions:

Version 0.3.0 (2016) and earlier require manual installation of ProteoWizard, and may require a Windows environment.

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:

* 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).

* 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>


GalaxyP Community
-----------------

Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:

<https://github.com/galaxyproteomics>


License
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Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.

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.

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/>.

You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.


Contributing
------------

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/>


Authors
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Authors and contributors:

* Björn Grüning
* Cody Wang
* Fred Sadler
* John Chilton <[e-mail]>
* Minnesota Supercomputing Institute, Univeristy of Minnesota
* Jeremy Volkening, University of Wisconsin-Madison