--- a/tools/protein_analysis/tmhmm2.xml	Wed Sep 18 06:16:58 2013 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Fri Nov 21 08:19:09 2014 -0500
@@ -1,13 +1,10 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.13">
     <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.
+      tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
       ##If the environment variable isn't set, get "", and the python wrapper
       ##defaults to four threads.
     </command>
@@ -119,4 +116,9 @@
 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>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1006/jmbi.2000.4315</citation>
+        <!-- TODO - add entry for PMID: 9783223 -->
+    </citations>
 </tool>