--- a/fimo.xml	Wed Jun 29 08:35:04 2016 -0400
+++ b/fimo.xml	Thu Jul 07 09:55:00 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.0.3">
+<tool id="meme_fimo" name="FIMO" version="4.11.0.4">
     <description>- Scan a set of sequences for motifs.</description>
     <requirements>
         <requirement type="package" version="6.9.3">imagemagick</requirement>
@@ -181,7 +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">
@@ -196,7 +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>