--- a/meme_chip.xml	Mon Apr 16 11:27:00 2018 -0400
+++ b/meme_chip.xml	Mon Apr 16 13:01:45 2018 -0400
@@ -11,76 +11,77 @@
 #set options_type = $options_type_cond.options_type
 meme-chip '$input'
 -noecho
-#if str($control):
+#if $control:
     -neg '$control'
 #end if
+$sequence_alphabet
 -o '$output.files_path'
 #if str($options_type)=='advanced':
     ## FIXME: CentriMo cannot be run,  See the comments in the input section.
     ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
     ## #if str($run_centrimo) == "yes":
     ##     -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_local):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_local:
     ##         -centrimo-local
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_score):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_score:
     ##         -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_maxreg):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
     ##         -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_ethresh):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
     ##         -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_noseq):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
     ##         -centrimo-noseq
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_flip):
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_flip:
     ##         -centrimo-flip
     ##     #end if
     ## #end if
-    #if str($options_type_cond.search_given_strand):
+    #if $options_type_cond.search_given_strand:
         -norc
     #end if
     -order $options_type_cond.background_model_order
     #if str($options_type_cond.subsampling_cond.subsampling) == "no":
         -norand
         #set seed = $options_type_cond.subsampling_cond.subsampling.seed
-        #if str($seed):
+        #if $seed:
             -seed $options_type_cond.subsampling_cond.subsampling.seed
         #end if
     #end if
-    #if str($options_type_cond.nmeme):
+    #if $options_type_cond.nmeme:
         -nmeme $options_type_cond.nmeme
     #end if
-    #if str($options_type_cond.ccut):
+    #if $options_type_cond.ccut:
         -ccut $options_type_cond.ccut
     #end if
     -group-thresh $options_type_cond.group_threash
-    #if str($options_type_cond.group_weak):
+    #if $options_type_cond.group_weak:
         -group-weak $options_type_cond.group_weak
     #end if
     -filter-thresh $options_type_cond.filter_thresh
-    #if str($options_type_cond.old_clustering):
+    #if $options_type_cond.old_clustering:
         -old-clustering
     #end if
     -meme-mod $options_type_cond.meme_mod
-    #if str($options_type_cond.meme_minw):
+    #if $options_type_cond.meme_minw:
         -meme-minw $options_type_cond.meme_minw
     #end if
-    #if str($options_type_cond.meme_maxw):
+    #if $options_type_cond.meme_maxw:
         -meme-maxw $options_type_cond.meme_maxw
     #end if
-    #if str($options_type_cond.meme_nmotifs):
+    #if $options_type_cond.meme_nmotifs:
         -meme-nmotifs $options_type_cond.meme_nmotifs
     #end if
-    #if str($options_type_cond.meme_minsites):
+    #if $options_type_cond.meme_minsites:
         -meme-minsites $options_type_cond.meme_minsites
     #end if
-    #if str($options_type_cond.meme_maxsites):
+    #if $options_type_cond.meme_maxsites:
         -meme-maxsites $options_type_cond.meme_maxsites
     #end if
-    #if str($options_type_cond.meme_pal):
+    #if $options_type_cond.meme_pal:
         -meme-pal
     #end if
     -dreme-e $options_type_cond.dreme_e
@@ -191,7 +192,7 @@
         </test>
         <test>
             <param name="input" value="input1.fasta" ftype="fasta"/>
-            <param name="sequence_alphabet" value="rna"/>
+            <param name="sequence_alphabet" value="-rna"/>
             <param name="options_type" value="advanced"/>
             <param name="background_model_order" value="0"/>
             <param name="non_commercial_use" value="True"/>