--- a/tools/protein_analysis/effectiveT3.xml	Tue Jun 07 16:32:23 2011 -0400
+++ b/tools/protein_analysis/effectiveT3.xml	Wed Apr 17 05:25:25 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.7">
+<tool id="effectiveT3" name="Effective T3" version="0.0.10">
     <description>Find bacterial effectors in protein sequences</description>
     <command interpreter="python">
 effectiveT3.py $module.fields.path
@@ -8,6 +8,11 @@
   $restrict.type
 #end if
 $fasta_file $tabular_file</command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <inputs>
         <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
         <param name="module" type="select" display="radio" label="Classification module">
@@ -33,6 +38,20 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="$module.value_label results" />
     </outputs>
+    <tests>
+        <test>
+            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="module" value="animal" />
+            <param name="type" value="selective" />
+            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
+            <param name="module" value="plant" />
+            <param name="type" value="sensistive" />
+            <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
+        </test>
+    </tests>
     <help>
     
 **What it does**
@@ -41,10 +60,15 @@
 
 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
 
- * Sequence identifier
- * Sequence description (from the FASTA file)
- * Score (between 0 and 1, or negative for an error such as a very short peptide)
- * Predicted effector (true/false)
+====== ==============================================================================
+Column Description
+------ ------------------------------------------------------------------------------
+     1 Sequence identifier
+     2 Sequence description (from the FASTA file)
+     3 Score (between 0 and 1, or negative for an error such as a very short peptide)
+     4 Predicted effector (true/false)
+====== ==============================================================================
+
 
 **References**