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Repository 'venn_list'
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
venn_list
unrestricted
Draw Venn Diagram (PDF) from lists, FASTA files, etc
Draw Venn Diagrams for 1, 2 or 3 sets of identifiers as a PDF file.

Can parse FASTA, FASTQ, SFF or tabular files (taking column one) for identifiers. This can be combined with Galaxy's extensive tabular file filtering and manipulation to prepare the input data.

Uses the R/Bioconductor package limma to draw the PDF file, called from Python with rpy.

Uses Biopython to parse SFF files.
3:6aae6bc0802d
peterjc
True
273

Repository README files - may contain important installation or license information

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.

Contents of this repository

Name Description Version
Venn Diagram from lists 0.0.6

Categories
Graphics
Sequence Analysis
Visualization