--- a/tools/protein_analysis/signalp3.xml	Tue Jun 07 17:41:38 2011 -0400
+++ b/tools/protein_analysis/signalp3.xml	Tue Mar 26 14:24:56 2013 -0400
@@ -1,9 +1,19 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.8">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.10">
     <description>Find signal peptides 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">
-      signalp3.py $organism $truncate 8 $fasta_file $tabular_file
-      ##I want the number of threads to be a Galaxy config option...
+      signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
+      ##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.
     </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
         <param name="organism" type="select" display="radio" label="Organism">