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Repository 'venn_list'
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/baf7031d470e
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.
0:baf7031d470e
peterjc
True
269

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 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. 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://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: tar -czf venn_list.tar.gz tools/plotting/venn_list.* Check this worked: $ tar -tzf venn_list.tar.gz tools/plotting/venn_list.py tools/plotting/venn_list.txt tools/plotting/venn_list.xml 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.

Contents of this repository

Name Description Version
Venn Diagram from lists 0.0.3

Automated tool test results

Time tested: 2014-02-13 12:57:51
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12484:b463c73f3348
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: venn_list
Tool version: 0.0.3
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.3
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for venn_list.

Categories
Graphics
Sequence Analysis
Visualization