annotate tools/filters/get_orfs_or_cdss.txt @ 2:324775a016ce draft

Uploaded v0.0.3, bundle Ssuis.fasta test file X record Python script version

Galaxy tool to find ORFs or simple CDSs
=======================================

This tool is copyright 2011-2013 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)

If you are installing this manually (rather than via the Tool Shed), 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. Then:

./run_functional_tests.sh -id get_orfs_or_cdss

That's it.


History
=======

v0.0.1 - Initial version.
v0.0.2 - Correct labelling issue on reverse strand.
       - Use the new <stdio> settings in the XML wrappers to catch errors
v0.0.3 - Include unit tests.
       - Record Python script version when run from Galaxy.


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://toolshed.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.* test-data/get_orf_input*.fasta test-data/Ssuis.fasta

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
test-data/get_orf_input.fasta
test-data/get_orf_input.Suis_ORF.nuc.fasta
test-data/get_orf_input.Suis_ORF.prot.fasta
test-data/get_orf_input.t11_nuc_out.fasta
test-data/get_orf_input.t11_open_nuc_out.fasta
test-data/get_orf_input.t11_open_prot_out.fasta
test-data/get_orf_input.t11_prot_out.fasta
test-data/get_orf_input.t1_nuc_out.fasta
test-data/get_orf_input.t1_prot_out.fasta
test-data/Ssuis.fasta


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.