--- a/tools/protein_analysis/effectiveT3.txt	Tue Jun 07 16:32:23 2011 -0400
+++ b/tools/protein_analysis/effectiveT3.txt	Wed Apr 17 05:25:25 2013 -0400
@@ -19,6 +19,10 @@
 
 http://effectors.org/
 
+
+Installation
+============
+
 You can change the path by editing the definition near the start of the Python
 script effectiveT3.py, but by default it expects the following files to be
 installed at these locations:
@@ -35,12 +39,18 @@
 * effectiveT3.py (the Python wrapper script)
 * effectiveT3.txt (this README file)
 
+Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
+(and edit if appropriate, e.g. to add or remove a model).
+
 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/effectiveT3.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.
 
 
@@ -48,6 +58,9 @@
 =======
 
 v0.0.7 - Initial public release
+v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
+v0.0.9 - Check the return code for errors in the XML
+v0.0.10- Added unit test
 
 
 Developers
@@ -56,10 +69,11 @@
 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 effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt
+$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
+
 
 Check this worked:
 
@@ -67,6 +81,11 @@
 tools/protein_analysis/effectiveT3.xml
 tools/protein_analysis/effectiveT3.py
 tools/protein_analysis/effectiveT3.txt
+tool-data/effectiveT3.loc.sample
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.effectiveT3.tabular
+test-data/empty.fasta
+test-data/empty_effectiveT3.tabular
 
 
 Licence (MIT/BSD style)
@@ -90,5 +109,5 @@
 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.
+NOTE: This is the licence for the Galaxy Wrapper only.
+EffectiveT3 is available and licenced separately.