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