--- a/tools/protein_analysis/nlstradamus.txt	Tue Jun 07 17:05:53 2011 -0400
+++ b/tools/protein_analysis/nlstradamus.txt	Wed Apr 17 08:25:23 2013 -0400
@@ -1,7 +1,7 @@
-Galaxy wrapper for NLStradamus v1.7 (C++ version)
-=================================================
+Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
+=========================================================
 
-This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute
+This wrapper 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.
 
@@ -11,15 +11,24 @@
 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://dx.doi.org/10.1186/1471-2105-10-202
 
 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.
+this point (early versions of NLStradamus came as a perl script only).
+
+Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
+unchanged.
+
 
-To install the wrapper installed the following files under the Galaxy tools
+Installation
+============
+This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
+PATH.
+
+To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a tools/protein_analysis folder:
 
 * nlstradamus.xml (the Galaxy tool definition)
@@ -31,6 +40,9 @@
 
 <tool file="protein_analysis/nlstradamus.xml" />
 
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder.
+
 That's it.
 
 
@@ -38,6 +50,11 @@
 =======
 
 v0.0.3 - Initial public release
+v0.0.4 - Adding DOI link to reference
+         (Documentation change only)
+v0.0.5 - Assume non-zero return codes are errors
+v0.0.6 - Show output help text using a table
+       - Added unit tests
 
 
 Developers
@@ -46,17 +63,20 @@
 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
+For making the "Galaxy Tool Shed" http://toolshed.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
+$ tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradamus.xml tools/protein_analysis/nlstradamus.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
 
 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
+tools/protein_analysis/nlstradamus.xml
+tools/protein_analysis/nlstradamus.txt
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.nlstradamus.tabular
+test-data/empty.fasta
+test-data/empty_nlstradamus.tabular
 
 
 Licence (MIT/BSD style)