--- a/cmsearch.xml	Tue Apr 22 13:56:22 2014 -0400
+++ b/cmsearch.xml	Thu Apr 24 15:02:05 2014 -0400
@@ -57,7 +57,7 @@
 
             ## 1. replace all lines starting # (comment lines)
             ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
-            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
+            sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
 
     </command>
         <inputs>