--- a/fimo.xml	Thu Jun 16 08:07:03 2016 -0400
+++ b/fimo.xml	Wed Jul 06 10:25:06 2016 -0400
@@ -1,8 +1,8 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.0.3">
+<tool id="meme_fimo" name="FIMO" version="4.11.1.0">
     <description>- Scan a set of sequences for motifs.</description>
     <requirements>
-        <requirement type="package" version="6.9.3">imagemagick</requirement>
-        <requirement type="package" version="4.11.0">meme</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="package" version="4.11.1">meme</requirement>
     </requirements>
     <command>
         <![CDATA[
@@ -117,7 +117,10 @@
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" />
+                        <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -178,7 +181,7 @@
             </actions>
         </data>
         <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)">
-            <filter>options_type['output_separate_motifs'] == 'no'</filter>
+            <filter>options_type['options_type_selector'] == 'basic' or (options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'no')</filter>
             <actions>
                 <conditional name="fasta_type.fasta_type_selector">
                     <when value="cached">
@@ -193,7 +196,7 @@
         </data>
         <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="gff" visible="false" />
-            <filter>options_type['output_separate_motifs'] == 'yes'</filter>
+            <filter>options_type['options_type_selector'] == 'advanced' and options_type['output_separate_motifs'] == 'yes'</filter>
         </collection>
         <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
             <actions>