--- a/tools/protein_analysis/tmhmm2.xml	Thu Apr 25 12:25:52 2013 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Wed Sep 18 06:16:58 2013 -0400
@@ -1,13 +1,15 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.10">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11">
     <description>Find transmembrane domains in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
       tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file
+      ##I want the number of threads to be a Galaxy config option...
       ##Set the number of threads in the runner entry in universe_wsgi.ini
       ##which (on SGE at least) will set the $NSLOTS environment variable.
-      ##If the environment variable isn't set, get "", and defaults to one.
+      ##If the environment variable isn't set, get "", and the python wrapper
+      ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -94,17 +96,27 @@
 
 **References**
 
-Krogh, Larsson, von Heijne, and Sonnhammer.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Krogh, Larsson, von Heijne, and Sonnhammer (2001).
 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
-J. Mol. Biol. 305:567-580, 2001.
+J. Mol. Biol. 305:567-580.
 http://dx.doi.org/10.1006/jmbi.2000.4315
 
-Sonnhammer, von Heijne, and Krogh.
+Sonnhammer, von Heijne, and Krogh (1998).
 A hidden Markov model for predicting transmembrane helices in protein sequences.
-In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.
+In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press.
 http://www.ncbi.nlm.nih.gov/pubmed/9783223
 
-http://www.cbs.dtu.dk/services/TMHMM/
+See also http://www.cbs.dtu.dk/services/TMHMM/
 
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
     </help>
 </tool>