diff tools/filters/get_orfs_or_cdss.txt @ 0:9cff9a1176ea

Uploaded v0.0.1

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+Galaxy tool to find ORFs or simple CDSs
+=======================================
+
+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 Biopython library functions)
+to search nucleotide sequences for open reading frames (ORFs) or coding
+sequences (CDSs) where the first potential start codon is used. See the
+help text in the XML file for more information.
+
+There are just two files to install:
+
+* get_orfs_or_cdss.py (the Python script)
+* get_orfs_or_cdss.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/filters next to the tool
+for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. One suggested location is in the filters section. Simply add the line:
+
+<tool file="filters/get_orfs_or_cdss.xml" />
+
+You will also need to install Biopython 1.54 or later. If you want to run
+the unit tests, include this line in tools_conf.xml.sample and the sample
+FASTA files under the test-data directory. That's it.
+
+
+History
+=======
+
+v0.0.1 - Initial version.
+
+
+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 get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.*
+
+Check this worked:
+
+$ tar -tzf get_orfs_or_cdss.tar.gz
+filter/get_orfs_or_cdss.py
+filter/get_orfs_or_cdss.txt
+filter/get_orfs_or_cdss.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.