Mercurial > repos > peterjc > venn_list
changeset 6:6ebfb498c2c4 draft
Uploaded v0.0.6 take 3, MIT licence, RST README, citation information
| author | peterjc |
|---|---|
| date | Wed, 11 Sep 2013 06:46:31 -0400 |
| parents | 51fe47a5a803 |
| children | 86bd05e9039b |
| files | test-data/venn_list1.pdf tools/plotting/venn_list.rst tools/plotting/venn_list.txt tools/plotting/venn_list.xml |
| diffstat | 4 files changed, 103 insertions(+), 84 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/plotting/venn_list.rst Wed Sep 11 06:46:31 2013 -0400 @@ -0,0 +1,93 @@ +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). +======= ====================================================================== + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/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.
--- a/tools/plotting/venn_list.txt Thu May 16 12:46:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -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 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" /> - -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. - - -History -======= - -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. - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/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.txt -tools/plotting/venn_list.xml -test-data/venn_list1.pdf -test-data/venn_list.tabular -test-data/rhodopsin_proteins.fasta - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE.
--- a/tools/plotting/venn_list.xml Thu May 16 12:46:18 2013 -0400 +++ b/tools/plotting/venn_list.xml Wed Sep 11 06:46:31 2013 -0400 @@ -105,9 +105,16 @@ The R library is called from Python via rpy, http://rpy.sourceforge.net/ -This tool uses Biopython to read SFF files. If you use this tool with -SFF files in scientific work leading to a publication, please cite the -Biopython application note: +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This tool uses Biopython to read and write SFF files, so you may also wish to +cite the Biopython application note (and Galaxy too of course): Cock et al 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.