Galaxy wrapper for NLStradamus v1.7 (C++ version)
=================================================

This wrapper 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.

NLStradamus is a command line tools for predicting nuclear localization
signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).

A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
BMC Bioinformatics. 2009 Jun 29;10(1):202.

http://www.moseslab.csb.utoronto.ca/NLStradamus

Early versions of NLStradamus did not have a native tabular output format, this
was added in version 1.7. Additionally a fast C++ implementation was added at
this point (early versions of NLStradamus came as a perl script only). This
wrapper expects the compiled C++ binary "NLStradamus" to be on the system PATH.

To install the wrapper installed the following files under the Galaxy tools
folder, e.g. in a tools/protein_analysis folder:

* nlstradamus.xml (the Galaxy tool definition)
* nlstradamus.txt (this README file)

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
tool. If you are using other protein analysis tools like TMHMM or SignalP, put
it next to them. Just add the line:

<tool file="protein_analysis/nlstradamus.xml" />

That's it.


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 nlstradmus.tar.gz tools/protein_analysis/nlstradum.xml tools/protein_analysis/nlstradum.txt

Check this worked:

$ tar -tzf nlstradmus.tar.gz
filter/seq_filter_by_id.py
filter/seq_filter_by_id.txt
filter/seq_filter_by_id.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.

NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
is available and licenced separately.