Mercurial > repos > pieterlukasse > prims_metabolomics
annotate README.rst @ 49:f772a5caa86a
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 10 Dec 2014 22:03:27 +0100 |
| parents | 664ccd5f7cf8 |
| children | 93102202ab79 |
| rev | line source |
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| 0 | 1 PRIMS-metabolomics toolset & Galaxy wrappers |
| 2 ============================================ | |
| 3 | |
| 4 Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. | |
| 5 This toolset consists of custom tools to enable metabolite identifications and | |
| 1 | 6 Retention Index (RI) based Quality Control (RIQC) for Mass Spectrometry metabolomics data. |
| 0 | 7 |
| 8 Copyright: | |
| 9 * 2012: NIST_UTIL and RIQC tools: Copyright (c) 2012 Maarten Kooyman and Marcel Kempenaar, NBIC BRS | |
| 10 * 2013: all tools: Copyright (c) 2013 by Pieter Lukasse, Plant Research International (PRI), | |
| 2 | 11 Wageningen, The Netherlands. All rights reserved. See the license text below. |
| 0 | 12 |
| 13 Galaxy wrappers and installation are available from the Galaxy Tool Shed at: | |
| 14 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics | |
| 15 | |
| 16 History | |
| 17 ======= | |
| 18 | |
| 19 ============== ====================================================================== | |
| 20 Date Changes | |
| 21 -------------- ---------------------------------------------------------------------- | |
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22 December 2014 * Added MsClust support for parsing XCMS alignment results. |
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23 * Improved output reports for XCMS wrappers. |
| 42 | 24 November 2014 * Added XCMS related tool wrappers (for metaMS and diffreport) |
| 40 | 25 September 2014 * Added new membership cutoff option for final clusters in MsClust |
| 26 * Improved MsClust memory usage for large datasets | |
| 27 * Simplified MsClust HTML report | |
| 38 | 28 * Added option for microminutes based clustering instead of scannr |
| 40 | 29 based in MsClust |
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30 April 2014 * Added interface to ExactMassDB, Pep1000, KEGG, KNApSAcK, Flavonoid |
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31 Viewer, LipidMAPS, HMDB, PubChem, by using the service MFSearcher. |
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32 This enables users to query multiple public repositories for |
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33 elemental compositions from accurate mass values detected by |
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34 high-resolution mass spectrometers. NB: see also added |
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35 licensing info below. |
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* Added interface to METEXP data store, including tool to fire queries in batch mode
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36 March 2014 * Added interface to METEXP data store, including tool to fire |
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37 queries in batch mode |
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38 * Improved quantification output files of MsClust, a.o. sorting |
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39 mass list based on intensity (last two columns of quantification |
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40 files) |
| 0 | 41 January 2014 * first release via Tool Shed, combining the RIQC and MsClust in a |
| 42 single package (this package) | |
| 43 * integration with METEXP software (data store for metabolomics | |
| 44 experiments with respective metadata and identifications) | |
| 45 2013 * hand-over of the NIST_UTIL and RIQC tools from the NBIC team to | |
| 46 Plant Research International | |
| 47 2012 * development of MsClust 2.0, making it also suitable for Galaxy | |
| 48 <2011 * development and publication of MsClust 1.0 | |
| 49 ============== ====================================================================== | |
| 50 | |
| 51 Tool Versioning | |
| 52 =============== | |
| 53 | |
| 54 PRIMS tools will have versions of the form X.Y.Z. Versions | |
| 55 differing only after the second decimal should be completely | |
| 56 compatible with each other. Breaking changes should result in an | |
| 57 increment of the number before and/or after the first decimal. All | |
| 58 tools of version less than 1.0.0 should be considered beta. | |
| 59 | |
| 60 | |
| 61 Bug Reports & other questions | |
| 62 ============================= | |
| 63 | |
| 64 For the time being issues can be reported via the contact form at: | |
| 65 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm | |
| 66 | |
| 67 Developers, Contributions & Collaborations | |
| 68 ========================================== | |
| 69 | |
| 70 If you wish to join forces and collaborate on some of the | |
| 71 tools do not hesitate to contact Pieter Lukasse via the contact form above. | |
| 72 | |
| 73 | |
| 74 License (Apache, Version 2.0) | |
| 75 ============================= | |
| 76 | |
| 77 Copyright 2013 Pieter Lukasse, Plant Research International (PRI). | |
| 78 | |
| 79 Licensed under the Apache License, Version 2.0 (the "License"); | |
| 80 you may not use this software except in compliance with the License. | |
| 81 You may obtain a copy of the License at | |
| 82 | |
| 83 http://www.apache.org/licenses/LICENSE-2.0 | |
| 84 | |
| 85 Unless required by applicable law or agreed to in writing, software | |
| 86 distributed under the License is distributed on an "AS IS" BASIS, | |
| 87 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| 88 See the License for the specific language governing permissions and | |
| 89 limitations under the License. | |
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90 |
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91 |
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92 License for third party services |
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93 ================================ |
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94 MFSearcher service : http://webs2.kazusa.or.jp/mfsearcher/#090 |
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95 In the MFSearcher system, the compound data provided by KEGG, Flavonoid Viewer, LIPID MAPS, HMDB and PubChem |
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96 were downloaded for academic purposes. The compound data of KNApSAcK is provided by Prof. Kanaya in |
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97 Nara Institute of Science and Technology (NAIST). The part of these data are utilized to construct the |
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98 specified databases for rapid mass searching in the MFSearcher system after re-calculating the molecular weights. |
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99 Please preserve the contracts of each original databases when utilizing the search results against these |
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100 databases by MFSearcher. |
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101 |
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102 The searching system of MFSearcher, the ExactMassDB database, and the Pep1000 database by Kazusa DNA |
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103 Research Institute is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. |