Mercurial > repos > peterjc > venn_list
comparison tools/plotting/venn_list.txt @ 0:aefc86eda5f6
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 17:42:40 -0400 |
| parents | |
| children | 29fcd027d67a |
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| -1:000000000000 | 0:aefc86eda5f6 |
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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. |