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comparison tools/plotting/venn_list.rst @ 3:6aae6bc0802d draft

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Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:19:51 -0400
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2:c96bef0643dc 3:6aae6bc0802d
1 Galaxy tool to draw a Venn Diagram with up to 3 sets
2 ====================================================
3
4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This tool is a short Python script (using both the Galaxy and Biopython library
9 functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
10 sets, which are then drawn using the R limma package function vennDiagram
11 (called from Python using rpy).
12
13 There are just two files to install:
14
15 * venn_list.py (the Python script)
16 * venn_list.xml (the Galaxy tool definition)
17
18 The suggested location is in the Galaxy folder tools/plotting next to other
19 graph drawing tools.
20
21 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
22 pacakge limma. You should already have rpy installed for other Galaxy tools.
23
24 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
25 tool. The suggested location is in the "Graph/Display Data" section. Simply add
26 the line::
27
28 <tool file="plotting/venn_list.xml" />
29
30 If you wish to run the unit tests, also add this to tools_conf.xml.sample and
31 move/copy the test-data files under Galaxy's test-data folder. Then::
32
33 ./run_functional_tests.sh -id venn_list
34
35
36 History
37 =======
38
39 ======= ======================================================================
40 Version Changes
41 ------- ----------------------------------------------------------------------
42 v0.0.3 - Initial public release.
43 v0.0.4 - Ignore blank lines when loading IDs from tabular files
44 v0.0.5 - Explicit Galaxy error handling of return codes
45 v0.0.6 - Added unit tests.
46 - Use reStructuredText for this README file.
47 - Adopt standard MIT licence.
48 - Updated citation information (Cock et al. 2013).
49 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
50 ======= ======================================================================
51
52
53 Developers
54 ==========
55
56 This script and related tools are being developed on the following hg branch:
57 http://bitbucket.org/peterjc/galaxy-central/src/tools
58
59 Development has now moved to a dedicated GitHub repository:
60 https://github.com/peterjc/pico_galaxy/tree/master/tools
61
62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
63 the following command from the Galaxy root folder::
64
65 $ tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
66
67 Check this worked::
68
69 $ tar -tzf venn_list.tar.gz
70 tools/plotting/venn_list.py
71 tools/plotting/venn_list.rst
72 tools/plotting/venn_list.xml
73 test-data/venn_list1.pdf
74 test-data/venn_list.tabular
75 test-data/rhodopsin_proteins.fasta
76
77
78 Licence (MIT)
79 =============
80
81 Permission is hereby granted, free of charge, to any person obtaining a copy
82 of this software and associated documentation files (the "Software"), to deal
83 in the Software without restriction, including without limitation the rights
84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
85 copies of the Software, and to permit persons to whom the Software is
86 furnished to do so, subject to the following conditions:
87
88 The above copyright notice and this permission notice shall be included in
89 all copies or substantial portions of the Software.
90
91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
97 THE SOFTWARE.