annotate README.rst @ 21:19d8fd10248e

* Added interface to METEXP data store, including tool to fire queries in batch mode * Improved quantification output files of MsClust, a.o. sorting mass list based on intensity (last two columns of quantification files) * Added Molecular Mass calculation method

PRIMS-metabolomics toolset & Galaxy wrappers
============================================
 
Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. 
This toolset consists of custom tools to enable metabolite identifications and 
Retention Index (RI) based Quality Control (RIQC) for Mass Spectrometry metabolomics data.

Copyright:
* 2012: NIST_UTIL and RIQC tools: Copyright (c) 2012 Maarten Kooyman and Marcel Kempenaar, NBIC BRS
* 2013: all tools: Copyright (c) 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_metabolomics

History
=======

============== ======================================================================
Date            Changes
-------------- ----------------------------------------------------------------------
March 2014     * Added interface to METEXP data store, including tool to fire 
                 queries in batch mode
               * Improved quantification output files of MsClust, a.o. sorting 
                 mass list based on intensity (last two columns of quantification
                 files)  
January 2014   * first release via Tool Shed, combining the RIQC and MsClust in a 
                 single package (this package)
               * integration with METEXP software (data store for metabolomics 
                 experiments with respective metadata and identifications)  
2013           * hand-over of the NIST_UTIL and RIQC tools from the NBIC team to  
                 Plant Research International  
2012           * development of MsClust 2.0, making it also suitable for Galaxy 
<2011          * development and publication of MsClust 1.0
============== ======================================================================

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.