--- a/meme_chip.xml	Mon Apr 16 13:01:45 2018 -0400
+++ b/meme_chip.xml	Fri Apr 20 09:03:24 2018 -0400
@@ -8,7 +8,6 @@
     <command detect_errors="exit_code"><![CDATA[
 #import os
 #set primary_output = $os.path.join($output.files_path, "index.html")
-#set options_type = $options_type_cond.options_type
 meme-chip '$input'
 -noecho
 #if $control:
@@ -16,7 +15,7 @@
 #end if
 $sequence_alphabet
 -o '$output.files_path'
-#if str($options_type)=='advanced':
+#if str($options_type_cond.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":
@@ -40,14 +39,11 @@
     ##         -centrimo-flip
     ##     #end if
     ## #end if
-    #if $options_type_cond.search_given_strand:
-        -norc
-    #end if
+    $options_type_cond.search_given_strand
     -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 $seed:
+        #if $options_type_cond.subsampling_cond.subsampling.seed:
             -seed $options_type_cond.subsampling_cond.subsampling.seed
         #end if
     #end if
@@ -58,13 +54,11 @@
         -ccut $options_type_cond.ccut
     #end if
     -group-thresh $options_type_cond.group_threash
-    #if $options_type_cond.group_weak:
+    #if str($options_type_cond.group_weak):
         -group-weak $options_type_cond.group_weak
     #end if
     -filter-thresh $options_type_cond.filter_thresh
-    #if $options_type_cond.old_clustering:
-        -old-clustering
-    #end if
+    $options_type_cond.old_clustering
     -meme-mod $options_type_cond.meme_mod
     #if $options_type_cond.meme_minw:
         -meme-minw $options_type_cond.meme_minw
@@ -81,9 +75,7 @@
     #if $options_type_cond.meme_maxsites:
         -meme-maxsites $options_type_cond.meme_maxsites
     #end if
-    #if $options_type_cond.meme_pal:
-        -meme-pal
-    #end if
+    $options_type_cond.meme_pal
     -dreme-e $options_type_cond.dreme_e
     -dreme-m $options_type_cond.dreme_m
     -spamo-skip
@@ -145,14 +137,14 @@
                     <option value="3">3rd order model of sequences</option>
                     <option value="4">4th order model of sequences</option>
                 </param>
-                <param name="nmeme" type="integer" optional="true" value="0" min="0" label="Limit of sequences to pass to MEME" help="Zero value has no effect"/>
+                <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/>
                 <conditional name="subsampling_cond">
                     <param name="subsampling" type="select" label="Should subsampling be random?" help="Select 'No' if your input sequences are sorted in order of confidence (best to worst)">
                         <option value="yes" selected="true">Yes</option>
                         <option value="no">No</option>
                     </param>
                     <when value="yes">
-                        <param name="seed" type="integer" optional="true" value="0" min="0" label="Seed for the randomized selection of sequences" help="Zero value indicates random seeding"/>
+                        <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -160,8 +152,8 @@
                 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
                 <param name="group_weak" type="float" optional="true" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
                 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
-                <param name="search_given_strand" type="boolean" truevalue="true" falsevalue="" checked="False" label="Search given strand only"/>
-                <param name="old_clustering" type="boolean" truevalue="true" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
+                <param name="search_given_strand" type="boolean" truevalue="-norc" falsevalue="" checked="False" label="Search given strand only"/>
+                <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
                 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
                     <option value="oops" selected="True">One occurance per sequence</option>
                     <option value="zoops">Zero or one occurances per sequence</option>
@@ -172,7 +164,7 @@
                 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/>
                 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/>
                 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/>
-                <param name="meme_pal" type="boolean" truevalue="true" falsevalue="" checked="False" label="Look for palindromes only"/>
+                <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/>
                 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
                 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
             </when>