annotate README.rst @ 55:543958f75e83

small fix
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 14:45:28 +0100
parents 93102202ab79
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 PRIMS-metabolomics toolset & Galaxy wrappers
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 ============================================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5 This toolset consists of custom tools to enable metabolite identifications and
1
e467a6c83d67 Initial commit to toolshed
pieter.lukasse@wur.nl
parents: 0
diff changeset
6 Retention Index (RI) based Quality Control (RIQC) for Mass Spectrometry metabolomics data.
0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8 Copyright:
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9 * 2012: NIST_UTIL and RIQC tools: Copyright (c) 2012 Maarten Kooyman and Marcel Kempenaar, NBIC BRS
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 * 2013: all tools: Copyright (c) 2013 by Pieter Lukasse, Plant Research International (PRI),
2
a35b55bfe96c small fix
pieter.lukasse@wur.nl
parents: 1
diff changeset
11 Wageningen, The Netherlands. All rights reserved. See the license text below.
0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 History
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17 =======
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19 ============== ======================================================================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20 Date Changes
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 -------------- ----------------------------------------------------------------------
50
93102202ab79 Added more options and better documentation.
pieter.lukasse@wur.nl
parents: 49
diff changeset
22 December 2014 * Added MsClust support for parsing XCMS alignment results.
49
f772a5caa86a Added more options and better documentation.
pieter.lukasse@wur.nl
parents: 42
diff changeset
23 * Improved output reports for XCMS wrappers.
42
664ccd5f7cf8 small fix for png method
pieter.lukasse@wur.nl
parents: 40
diff changeset
24 November 2014 * Added XCMS related tool wrappers (for metaMS and diffreport)
40
a7b609941846 updated text
pieter.lukasse@wur.nl
parents: 38
diff changeset
25 September 2014 * Added new membership cutoff option for final clusters in MsClust
a7b609941846 updated text
pieter.lukasse@wur.nl
parents: 38
diff changeset
26 * Improved MsClust memory usage for large datasets
a7b609941846 updated text
pieter.lukasse@wur.nl
parents: 38
diff changeset
27 * Simplified MsClust HTML report
38
7ebc61adb47e updated readme
pieter.lukasse@wur.nl
parents: 24
diff changeset
28 * Added option for microminutes based clustering instead of scannr
40
a7b609941846 updated text
pieter.lukasse@wur.nl
parents: 38
diff changeset
29 based in MsClust
24
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
30 April 2014 * Added interface to ExactMassDB, Pep1000, KEGG, KNApSAcK, Flavonoid
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
31 Viewer, LipidMAPS, HMDB, PubChem, by using the service MFSearcher.
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
32 This enables users to query multiple public repositories for
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
33 elemental compositions from accurate mass values detected by
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
34 high-resolution mass spectrometers. NB: see also added
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
35 licensing info below.
21
19d8fd10248e * Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents: 2
diff changeset
36 March 2014 * Added interface to METEXP data store, including tool to fire
19d8fd10248e * Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents: 2
diff changeset
37 queries in batch mode
19d8fd10248e * Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents: 2
diff changeset
38 * Improved quantification output files of MsClust, a.o. sorting
19d8fd10248e * Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents: 2
diff changeset
39 mass list based on intensity (last two columns of quantification
19d8fd10248e * Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents: 2
diff changeset
40 files)
0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41 January 2014 * first release via Tool Shed, combining the RIQC and MsClust in a
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 single package (this package)
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
43 * integration with METEXP software (data store for metabolomics
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
44 experiments with respective metadata and identifications)
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
45 2013 * hand-over of the NIST_UTIL and RIQC tools from the NBIC team to
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
46 Plant Research International
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
47 2012 * development of MsClust 2.0, making it also suitable for Galaxy
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
48 <2011 * development and publication of MsClust 1.0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
49 ============== ======================================================================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
50
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
51 Tool Versioning
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
52 ===============
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
53
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
54 PRIMS tools will have versions of the form X.Y.Z. Versions
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
55 differing only after the second decimal should be completely
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
56 compatible with each other. Breaking changes should result in an
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
57 increment of the number before and/or after the first decimal. All
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
58 tools of version less than 1.0.0 should be considered beta.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
59
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
60
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
61 Bug Reports & other questions
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
62 =============================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
63
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
64 For the time being issues can be reported via the contact form at:
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
65 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
66
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
67 Developers, Contributions & Collaborations
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
68 ==========================================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
69
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
70 If you wish to join forces and collaborate on some of the
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
71 tools do not hesitate to contact Pieter Lukasse via the contact form above.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
72
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
73
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
74 License (Apache, Version 2.0)
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
75 =============================
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
76
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
77 Copyright 2013 Pieter Lukasse, Plant Research International (PRI).
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
78
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
79 Licensed under the Apache License, Version 2.0 (the "License");
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
80 you may not use this software except in compliance with the License.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
81 You may obtain a copy of the License at
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
82
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
83 http://www.apache.org/licenses/LICENSE-2.0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
84
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
85 Unless required by applicable law or agreed to in writing, software
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
86 distributed under the License is distributed on an "AS IS" BASIS,
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
87 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
88 See the License for the specific language governing permissions and
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
89 limitations under the License.
24
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
90
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
91
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
92 License for third party services
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
93 ================================
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
94 MFSearcher service : http://webs2.kazusa.or.jp/mfsearcher/#090
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
95 In the MFSearcher system, the compound data provided by KEGG, Flavonoid Viewer, LIPID MAPS, HMDB and PubChem
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
96 were downloaded for academic purposes. The compound data of KNApSAcK is provided by Prof. Kanaya in
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
97 Nara Institute of Science and Technology (NAIST). The part of these data are utilized to construct the
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
98 specified databases for rapid mass searching in the MFSearcher system after re-calculating the molecular weights.
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
99 Please preserve the contracts of each original databases when utilizing the search results against these
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
100 databases by MFSearcher.
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
101
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
102 The searching system of MFSearcher, the ExactMassDB database, and the Pep1000 database by Kazusa DNA
385d21a8d0a0 New tool to Query multiple public repositories for elemental compositions
pieter.lukasse@wur.nl
parents: 21
diff changeset
103 Research Institute is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.