comparison tools/plotting/venn_list.txt @ 0:baf7031d470e

Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:08:11 -0400
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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 modify the tools_conf.xml file to tell Galaxy to offer the
22 tool. The suggested location is in the "Graph/Display Data" section. Simply add
23 the line:
24
25 <tool file="plotting/venn_list.xml" />
26
27 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
28 pacakge limma. You should already have rpy installed for other Galaxy tools.
29
30
31 History
32 =======
33
34 v0.0.3 - Initial public release.
35
36
37 Developers
38 ==========
39
40 This script and related tools are being developed on the following hg branch:
41 http://bitbucket.org/peterjc/galaxy-central/src/tools
42
43 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
44 the following command from the Galaxy root folder:
45
46 tar -czf venn_list.tar.gz tools/plotting/venn_list.*
47
48 Check this worked:
49
50 $ tar -tzf venn_list.tar.gz
51 tools/plotting/venn_list.py
52 tools/plotting/venn_list.txt
53 tools/plotting/venn_list.xml
54
55
56 Licence (MIT/BSD style)
57 =======================
58
59 Permission to use, copy, modify, and distribute this software and its
60 documentation with or without modifications and for any purpose and
61 without fee is hereby granted, provided that any copyright notices
62 appear in all copies and that both those copyright notices and this
63 permission notice appear in supporting documentation, and that the
64 names of the contributors or copyright holders not be used in
65 advertising or publicity pertaining to distribution of the software
66 without specific prior permission.
67
68 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
69 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
70 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
71 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
72 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
73 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
74 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
75 OR PERFORMANCE OF THIS SOFTWARE.