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README.rst
README.rst
 
 
venn_list.py
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venn_list.xml
venn_list.xml
 
 

README.rst

Galaxy tool to draw a Venn Diagram with up to 3 sets

This tool is copyright 2011-2023 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).

This tool is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list

Automated Installation

This should be straightforward, Galaxy should automatically download the tool and the Python dependencies Biopython and rpy, and the R/Bioconductor package limma.

Manual Installation

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, or a dedicated tools/venn_list directory.

You will also need to install Biopython 1.54 or later, matplotlib, and matplotlib_venn - all available via PyPI or Conda,

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="venn_list/venn_list.xml" />

If you wish to run the unit tests, also move/copy the test-data/ files under Galaxy's test-data/ folder. Then:

./run_tests.sh -id venn_list

History

Version Changes
v0.1.2
  • Fixed file open mode for Python 3.11 onwards.
v0.1.1
  • Removed legacy tool_dependencies.xml file (the legacy Galaxy packages did not cover matplotlib_venn anyway).
v0.1.0
  • Now uses Python library matplotlib_venn to draw the diagram instead of R's limma via rpy). Contribution from Frederic Sapet.
v0.0.12
  • Internal Python style change.
  • Python 3 compatible exception handling.
v0.0.11
  • Use <command detect_errors="aggressive"> (internal change only).
  • Single quote command line arguments (internal change only)
  • Python 3 compatible print function.
  • Capture python script version when run from Galaxy.
v0.0.10
  • Updated to point at Biopython 1.67 (latest version in Tool Shed).
  • Explicit dependency on galaxy_sequence_utils.
  • Python style updates (internal change only).
v0.0.9
  • Test with three-way Venn diagram.
  • Includes testing of failure mode.
  • Planemo for Tool Shed upload (.shed.yml, internal change only).
v0.0.8
  • Reorder XML elements (internal change only).
  • Fixed and improved error handling when rpy is not available.
  • Test output relaxed to cope with more variation in PDF output.
  • Declare Biopython dependency via the Tool Shed.
v0.0.7
  • Renamed folder and README file.
  • Tool definition now embeds citation information.
v0.0.6
v0.0.5
  • Explicit Galaxy error handling of return codes
v0.0.4
  • Ignore blank lines when loading IDs from tabular files
v0.0.3
  • Initial public release.

Developers

This script and related tools were initially 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

For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ~/.planemo.yml and that you have access rights on the Tool Shed):

$ planemo shed_update -t testtoolshed --check_diff tools/venn_list/
...

or:

$ planemo shed_update -t toolshed --check_diff tools/venn_list/
...

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/venn_list/
...
$ tar -tzf shed_upload.tar.gz
tools/venn_list/README.rst
tools/venn_list/tool_dependencies.xml
tools/venn_list/venn_list.py
tools/venn_list/venn_list.xml
test-data/magic.pdf
test-data/rhodopsin_proteins.fasta
test-data/venn_list.tabular

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.