PRIMS-masscomb toolset & Galaxy wrappers
========================================

MASSCOMB module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. 

This toolset consists of tools that enable combining popular external mass spectrometry 
data processing tools (like X!Tandem and ProteoWizard's MsPicture) 
into your own Galaxy workflows. 

Can be used a.o. in combination with PRIMV-visualization (primv_visualization package) and
PRIMS-proteomics (prims_proteomics package).

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

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


History
=======

============== ========================================================================
Date            Changes
-------------- ------------------------------------------------------------------------
January 2014   * first release via Tool Shed
November 2013  * tools used internally at PRI 
...            ... 
December 2011  * added wrapper for X!Tandem and tool for converting output to MzIdentML
============== ========================================================================

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

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.

License of third party software used
====================================
For X!Tandem see the license included in this repository:
http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/file/tip/XTANDEM_README.txt
          
For ProteoWizard see the license included in this repository:
http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/file/tip/PROTEOWIZARD_LICENSE.txt