view README.rst @ 0:a9e90cdcb97a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty

GalaxyP - PeptideShaker
=======================

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


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

Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker.

Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these.  It creates a large zip archive with all search results, the original database and spectra.  This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.


Configuration
-------------

This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:

    export _JAVA_OPTIONS='-Xmx1500M'

On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:

	export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'

It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.

Note:

- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.

See:

* <https://code.google.com/p/peptide-shaker/>
* <https://code.google.com/p/searchgui/>


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

Current governing community policies for GalaxyP_ and other information can be found at:

<https://github.com/galaxyproteomics>

.. _GalaxyP: https://github.com/galaxyproteomics/


License
-------

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
-------

Authors and contributors:

* Bjoern Gruening <[e-mail]>
* Ira Cooke
* Cody Wang
* Fred Sadler
* John Chilton <[e-mail]>
* Minnesota Supercomputing Institute, Univeristy of Minnesota