# HG changeset patch
# User peterjc
# Date 1378896391 14400
# Node ID 6ebfb498c2c404dc48e06c67ee1f0781505b63a6
# Parent 51fe47a5a8033a95796ce5eead2fbf6b1c28254c
Uploaded v0.0.6 take 3, MIT licence, RST README, citation information
diff -r 51fe47a5a803 -r 6ebfb498c2c4 test-data/venn_list1.pdf
Binary file test-data/venn_list1.pdf has changed
diff -r 51fe47a5a803 -r 6ebfb498c2c4 tools/plotting/venn_list.rst
--- /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::
+
+
+
+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.
diff -r 51fe47a5a803 -r 6ebfb498c2c4 tools/plotting/venn_list.txt
--- 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:
-
-
-
-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.
diff -r 51fe47a5a803 -r 6ebfb498c2c4 tools/plotting/venn_list.xml
--- 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.