--- a/tRNAscan.xml	Sat Jul 06 10:37:13 2013 -0400
+++ b/tRNAscan.xml	Thu Jan 22 13:15:51 2015 -0500
@@ -5,6 +5,7 @@
         <requirement type="package" version="1.61">biopython</requirement>
     </requirements>
     <command interpreter="python">
+<![CDATA[
         tRNAscan.py
             $organism
             $mode
@@ -15,6 +16,7 @@
             $tabular_output
             $inputfile
             $fasta_output
+]]>
     </command>
     <inputs>
         <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
@@ -54,6 +56,7 @@
         </test>
     </tests>
     <help>
+<![CDATA[
 
 
 .. class:: warningmark
@@ -176,7 +179,7 @@
 	pseudogene. The heuristic pseudogene detection filter uses this
 	information to flag possible pseudogenes -- use this option to see why
 	a hit is marked as a possible pseudogene. The user may wish to
-	examine score breakdowns from known tRNAs in the organism of interest 
+	examine score breakdowns from known tRNAs in the organism of interest
 	to get a frame of reference.
 
 -----
@@ -207,7 +210,7 @@
 
 
     ========     ======    =====     ======    ====    ==========    ======    ======    ==========    ==========
-                              tRNA Bounds                              Intron Bonds                              
+                              tRNA Bounds                              Intron Bonds
     --------     ------    ----------------    ----    ----------    ----------------    ----------    ----------
     Name         # tRNA    Begin     End       tRNA    Anti Codon    Begin     End       Cove Score    Hit Origin
     ========     ======    =====     ======    ====    ==========    ======    ======    ==========    ==========
@@ -227,8 +230,9 @@
 
 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
 
-doi:10.1093/nar/25.5.0955 
+doi:10.1093/nar/25.5.0955
 
 
+]]>
     </help>
 </tool>