diff tools/plotting/venn_list.rst @ 6:6ebfb498c2c4 draft

Uploaded v0.0.6 take 3, MIT licence, RST README, citation information

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+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.