--- a/tools/protein_analysis/psortb.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Thu May 23 12:49:18 2013 -0400
@@ -1,10 +1,17 @@
-<tool id="Psortb" name="psortb" version="0.0.2">
+<tool id="Psortb" name="psortb" version="0.0.3">
   <description>Determines sub-cellular localisation of bacterial/archaeal 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>
   <version_command interpreter="python">psortb.py --version</version_command>
-  <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
+  <command interpreter="python">
+    psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
+    ##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 python wrapper
+    ##defaults to four threads.
+  </command>
   <stdio>
     <!-- Anything other than zero is an error -->
     <exit_code range="1:" />