PRIMS-proteomics toolset & Galaxy wrappers
==========================================
 
Proteomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. 
This toolset consists of custom tools to enable data processing and 
protein inference for labeled and label-free Mass Spectrometry proteomics data. 

Can be used in combination with PRIMS-MASSCOMB (prims_masscomb package) and
with PRIMV-visualization (primv_visualization package).

Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), 
Wageningen, The Netherlands. All rights reserved. See the license text below.

Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_proteomics

History
=======

============== ======================================================================
Date            Changes
-------------- ----------------------------------------------------------------------
April  2014    * Added support for pepxml (and more specifically for 
                 ProteomeDiscoverer 1.4). Tested with ProteomeDiscoverer 1.4 pepxml. 
               * Improved HTML report of NapQ tool.
               * Fixed issue that was preventing SEDMAT matching from running  
                 in parallel/multi-threaded.  
January 2014   * first release via Tool Shed
November 2013  * multiple tools used internally at PRI 
end 2011       * first tool
============== ======================================================================

Tool Versioning
===============

PRIMS tools will have versions of the form X.Y.Z. Versions
differing only after the second decimal should be completely
compatible with each other. Breaking changes should result in an
increment of the number before and/or after the first decimal. All
tools of version less than 1.0.0 should be considered beta.


Bug Reports & other questions
=============================

For the time being issues can be reported via the contact form at:
http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm

Developers, Contributions & Collaborations 
==========================================

If you wish to join forces and collaborate on some of the 
tools do not hesitate to contact Pieter Lukasse via the contact form above. 


License (Apache, Version 2.0)
=============================

Copyright 2013 Pieter Lukasse, Plant Research International (PRI). 

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this software except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.