diff tools/plotting/venn_list.txt @ 0:aefc86eda5f6

Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository

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+++ b/tools/plotting/venn_list.txt	Tue Jun 07 17:42:40 2011 -0400
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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 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" />
+
+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.