--- a/tools/protein_analysis/clinod.xml	Tue Aug 02 06:51:52 2011 -0400
+++ b/tools/protein_analysis/clinod.xml	Tue Apr 16 13:01:54 2013 -0400
@@ -1,10 +1,15 @@
-<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1">
+<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.4">
     <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
     <command>
       java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence
       ##I want the number of threads to be a Galaxy config option...
-      ##TODO - Make the -clean_sequece argument a parameter?
+      ##TODO - Make the -clean_sequence argument a parameter?
     </command>
+    <stdio>
+        <!-- Assume 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"/> 
     </inputs>
@@ -14,8 +19,14 @@
     <requirements>
         <requirement type="binary">java</requirement>
     </requirements>
+    <tests>
+        <test>
+            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
+	    <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
+        </test>
+    </tests>
     <help>
-    
+
 **What it does**
 
 This calls the command line version of the NoD tool from the Barton Group for
@@ -28,14 +39,19 @@
 The input is a FASTA file of protein sequences, and the output is tabular with
 four columns (multiple rows per protein):
 
- * Sequence identifier
- * Start of NoLS
- * End of NoLS
- * NoLS sequence
+====== ===================
+Column Description
+------ -------------------
+     1 Sequence identifier
+     2 Start of NoLS
+     3 End of NoLS
+     4 NoLS sequence
+====== ===================
 
 If a sequence has no predicted NoLS, then there is no line in the output file
 for it.
 
+
 **References**
 
 M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
@@ -45,7 +61,8 @@
 
 M. S. Scott, P. V. Troshin and G. J. Barton.
 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
-BMC Bioinformatics, in press, 2011.
+BMC Bioinformatics, 12:317, 2011.
+http://dx.doi.org/10.1186/1471-2105-12-317
 
 http://www.compbio.dundee.ac.uk/www-nod/