Mercurial > repos > peterjc > venn_list
diff 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 |
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date | Wed, 18 Sep 2013 06:19:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/plotting/venn_list.rst Wed Sep 18 06:19:51 2013 -0400 @@ -0,0 +1,97 @@ +Galaxy tool to draw a Venn Diagram with up to 3 sets +==================================================== + +This tool is copyright 2011 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using both the Galaxy and Biopython library +functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build +sets, which are then drawn using the R limma package function vennDiagram +(called from Python using rpy). + +There are just two files to install: + +* venn_list.py (the Python script) +* venn_list.xml (the Galaxy tool definition) + +The suggested location is in the Galaxy folder tools/plotting next to other +graph drawing tools. + +You will also need to install Biopython 1.54 or later, and the R/Bioconductor +pacakge limma. You should already have rpy installed for other Galaxy tools. + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. The suggested location is in the "Graph/Display Data" section. Simply add +the line:: + + <tool file="plotting/venn_list.xml" /> + +If you wish to run the unit tests, also add this to tools_conf.xml.sample and +move/copy the test-data files under Galaxy's test-data folder. Then:: + + ./run_functional_tests.sh -id venn_list + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.3 - Initial public release. +v0.0.4 - Ignore blank lines when loading IDs from tabular files +v0.0.5 - Explicit Galaxy error handling of return codes +v0.0.6 - Added unit tests. + - Use reStructuredText for this README file. + - Adopt standard MIT licence. + - Updated citation information (Cock et al. 2013). + - Development moved to GitHub, https://github.com/peterjc/pico_galaxy +======= ====================================================================== + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +Development has now moved to a dedicated GitHub repository: +https://github.com/peterjc/pico_galaxy/tree/master/tools + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder:: + + $ 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 + +Check this worked:: + + $ tar -tzf venn_list.tar.gz + tools/plotting/venn_list.py + tools/plotting/venn_list.rst + tools/plotting/venn_list.xml + test-data/venn_list1.pdf + test-data/venn_list.tabular + test-data/rhodopsin_proteins.fasta + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.