--- a/tools/protein_analysis/nlstradamus.xml	Tue Jun 07 17:39:58 2011 -0400
+++ b/tools/protein_analysis/nlstradamus.xml	Wed Apr 17 08:26:25 2013 -0400
@@ -1,8 +1,13 @@
-<tool id="nlstradamus" name="NLStradamus" version="0.0.3">
+<tool id="nlstradamus" name="NLStradamus" version="0.0.6">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
     <command>
       NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
     </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"/> 
         <param name="model" type="select" display="radio" label="Model">
@@ -25,6 +30,20 @@
         <requirement type="binary">NLStradamus</requirement>
     </requirements>
     <tests>
+        <test>
+            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="model" value="1" />
+            <param name="algorithm" value="1" />
+	    <param name="threshold" value="0.6" />
+            <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
+            <param name="model" value="2" />
+            <param name="algorithm" value="2" />
+            <param name="threshold" value="0.125"/>
+            <output name="tabular_file" file="empty_nlstradamus.tabular" ftype="tabular" />
+        </test>
     </tests>
     <help>
     
@@ -36,12 +55,16 @@
 The input is a FASTA file of protein sequences, and the output is tabular
 with six columns (one row per NLS):
 
- * Sequence identifier
- * Algorithm (posterior or Viterbi)
- * Score (probability between threshold and 1 for posterior algorithm)
- * Start
- * End
- * Sequence of NLS
+====== ===================================================================
+Column Description
+------ -------------------------------------------------------------------
+    c1 Sequence identifier
+    c2 Algorithm (posterior or Viterbi)
+    c3 Score (probability between threshold and 1 for posterior algorithm)
+    c4 Start
+    c5 End
+    c6 Sequence of NLS
+====== ===================================================================
 
 -----
 
@@ -50,6 +73,7 @@
 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
 BMC Bioinformatics. 2009 Jun 29;10(1):202.
+http://dx.doi.org/10.1186/1471-2105-10-202
 
 http://www.moseslab.csb.utoronto.ca/NLStradamus