view tools/filters/get_orfs_or_cdss.rst @ 4:d51819d2d7e2 draft

Uploaded correct tar ball (v0.0.5)

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.

This tool is available from the Galaxy Tool Shed at:

* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss

See also the EMBOSS tool ``getorf`` which offers similar functionality and
has also been wrapped for use within Galaxy.


Automated Installation
======================

This should be straightforward using the Galaxy Tool Shed, which should be
able to automatically install the dependency on Biopython, and then install
this tool and run its unit tests.


Manual Installation
===================

There are just two files to install to use this tool from within Galaxy:

* 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
=======

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
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.
v0.0.4   - Link to Tool Shed added to help text and this documentation.
v0.0.5   - Automated intallation of the Biopython dependency.
         - Use reStructuredText for this README file.
         - Adopt standard MIT License.
======= ======================================================================


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.* tools/filters/repository_dependencies.xml 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.rst
    filter/get_orfs_or_cdss.xml
    tools/filters/repository_dependencies.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)
=============

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.