--- a/meme_chip.xml	Thu Jul 12 08:48:01 2018 -0400
+++ b/meme_chip.xml	Thu Nov 15 09:57:52 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="meme_chip" name="MEME-ChIP" version="4.11.2">
+<tool id="meme_chip" name="MEME-ChIP" version="@WRAPPER_VERSION@+galaxy1">
     <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
     <macros>
         <import>macros.xml</import>
@@ -16,27 +16,29 @@
 $sequence_alphabet
 -o '$output.files_path'
 #if str($options_type_cond.options_type)=='advanced':
-    #if str($options_type_cond.run_centrimo_cond.run_centrimo) == "yes":
-        -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
-        #if $options_type_cond.run_centrimo_cond.centrimo_local:
-            -centrimo-local
-        #end if
-        #if $options_type_cond.run_centrimo_cond.centrimo_score:
-            -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
-        #end if
-        #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
-            -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
-        #end if
-        #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
-            -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
-        #end if
-        #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
-            -centrimo-noseq
-        #end if
-        #if $options_type_cond.run_centrimo_cond.centrimo_flip:
-            -centrimo-flip
-        #end if
-    #end if
+    ## 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 $options_type_cond.run_centrimo_cond.centrimo_local:
+    ##         -centrimo-local
+    ##     #end if
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_score:
+    ##         -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
+    ##     #end if
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
+    ##         -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
+    ##     #end if
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
+    ##         -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
+    ##     #end if
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
+    ##         -centrimo-noseq
+    ##     #end if
+    ##     #if $options_type_cond.run_centrimo_cond.centrimo_flip:
+    ##         -centrimo-flip
+    ##     #end if
+    ## #end if
     $options_type_cond.search_given_strand
     -order $options_type_cond.background_model_order
     #if str($options_type_cond.subsampling_cond.subsampling) == "no":
@@ -79,8 +81,7 @@
     -spamo-skip
     -fimo-skip
 #end if
-&& rm '$output'
-&& ln -s $primary_output '$output'
+&& mv $primary_output '$output'
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
@@ -96,16 +97,23 @@
             </param>
             <when value="basic"/>
             <when value="advanced">
+                <!--
+                FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
                 <conditional name="run_centrimo_cond">
                     <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
                         <option value="yes" selected="true">Yes</option>
                         <option value="no">No</option>
                     </param>
                     <when value="yes">
+
+                        We have 2 dynamic select lists here.  The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
+                        data table.  The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
+                        select list is changed.  This composition used to work (see Examples->Dynamic Options section of
+                        https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does.  We'll have to figure out what is broken in
+                        the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
+
                         <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
                             <options from_data_table="meme_motif_databases">
-                                <column name="name" index="1"/>
-                                <column name="value" index="2"/>
                                 <filter type="sort_by" column="1"/>
                                 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
                             </options>
@@ -120,6 +128,7 @@
                     </when>
                     <when value="no"/>
                 </conditional>
+                -->
                 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
                     <option value="0">0-order model of sequences</option>
                     <option value="1" selected="True">1st order model of sequences</option>