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+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.
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