annotate README.rst @ 9:c317e0f939df

Made converter more robust and added support for mzXML in xtandem interface
author pieter.lukasse@wur.nl
date Fri, 07 Feb 2014 11:41:58 +0100
parents d6001e8d7441
children f47b24cccf88
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 PRIMS-masscomb toolset & Galaxy wrappers
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 ========================================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 MASSCOMB module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
6 This toolset consists of tools that enable combining popular external mass spectrometry
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7 data processing tools (like X!Tandem and ProteoWizard's MsPicture)
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8 into your own Galaxy workflows.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 Can be used a.o. in combination with PRIMV-visualization (primv_visualization package) and
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
11 PRIMS-proteomics (prims_proteomics package).
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI),
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14 Wageningen, The Netherlands. All rights reserved. See the license text in LICENSE file.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 Galaxy wrappers and installation are available from the Galaxy Tool Shed at:
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17 http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20 History
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 =======
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
22
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
23 ============== ========================================================================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
24 Date Changes
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
25 -------------- ------------------------------------------------------------------------
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
26 January 2014 * first release via Tool Shed
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
27 November 2013 * tools used internally at PRI
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
28 ... ...
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
29 December 2011 * added wrapper for X!Tandem and tool for converting output to MzIdentML
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
30 ============== ========================================================================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
31
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
32 Tool Versioning
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
33 ===============
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
34
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
35 Tools will have versions of the form X.Y.Z. Versions
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
36 differing only after the second decimal should be completely
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
37 compatible with each other. Breaking changes should result in an
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
38 increment of the number before and/or after the first decimal. All
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
39 tools of version less than 1.0.0 should be considered beta.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
40
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 Bug Reports & other questions
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
43 =============================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
44
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
45 For the time being issues can be reported via the contact form at
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
46 http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
47
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
48 Developers, Contributions & Collaborations
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
49 ==========================================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
50
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
51 If you wish to join forces and collaborate on some of the
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
52 tools do not hesitate to contact Pieter Lukasse via the contact form above.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
53
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
54 License (Apache, Version 2.0)
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
55 =============================
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
56
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
57 Copyright 2013 Pieter Lukasse, Plant Research International (PRI).
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
58
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
59 Licensed under the Apache License, Version 2.0 (the "License");
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
60 you may not use this software except in compliance with the License.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
61 You may obtain a copy of the License at
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
62
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
63 http://www.apache.org/licenses/LICENSE-2.0
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
64
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
65 Unless required by applicable law or agreed to in writing, software
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
66 distributed under the License is distributed on an "AS IS" BASIS,
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
67 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
68 See the License for the specific language governing permissions and
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
69 limitations under the License.
d6001e8d7441 Push to main toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
70