annotate README.rst @ 50:93102202ab79

Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.

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
-------------- ----------------------------------------------------------------------
December 2014  * Added MsClust support for parsing XCMS alignment results. 
               * Improved output reports for XCMS wrappers.
November 2014  * Added XCMS related tool wrappers (for metaMS and diffreport)
September 2014 * Added new membership cutoff option for final clusters in MsClust
               * Improved MsClust memory usage for large datasets 
               * Simplified MsClust HTML report
               * Added option for microminutes based clustering instead of scannr
                 based in MsClust
April 2014     * Added interface to ExactMassDB, Pep1000, KEGG, KNApSAcK, Flavonoid 
                 Viewer, LipidMAPS, HMDB, PubChem, by using the service MFSearcher.
                 This enables users to query multiple public repositories for 
                 elemental compositions from accurate mass values detected by 
                 high-resolution mass spectrometers. NB: see also added 
                 licensing info below. 
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.


License for third party services
================================
MFSearcher service : http://webs2.kazusa.or.jp/mfsearcher/#090 
In the MFSearcher system, the compound data provided by KEGG, Flavonoid Viewer, LIPID MAPS, HMDB and PubChem 
were downloaded for academic purposes. The compound data of KNApSAcK is provided by Prof. Kanaya in 
Nara Institute of Science and Technology (NAIST). The part of these data are utilized to construct the 
specified databases for rapid mass searching in the MFSearcher system after re-calculating the molecular weights. 
Please preserve the contracts of each original databases when utilizing the search results against these 
databases by MFSearcher.     

The searching system of MFSearcher, the ExactMassDB database, and the Pep1000 database by Kazusa DNA 
Research Institute is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.