--- a/tools/protein_analysis/tmhmm2.xml	Tue Jun 07 17:37:26 2011 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Tue Jun 07 17:38:05 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.1">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.3">
     <description>Find transmembrane domains in protein sequences</description>
     <command interpreter="python">
       tmhmm2.py 8 $fasta_file $tabular_file
@@ -22,7 +22,11 @@
     <tests>
         <test>
             <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
-            <output name="tabular_file" file="four_human_proteins.tmhmm2.tsv" ftype="tabular"/>
+            <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
+            <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/>
         </test>
     </tests>
     <help>
@@ -40,9 +44,9 @@
  5. Number of transmembrane helices predicted by N-best.
  6. Topology predicted by N-best (encoded as a strip using o for output and i for inside)
 
-Predicted TM segments in the n-terminal region sometime turn out to be signal peptides.
+Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.
 
-One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment.
+One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment (i.e. mixing up which end of the protein is outside and inside the membrane).
 
 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.