--- a/meme_chip.xml	Thu Mar 15 13:16:40 2018 -0400
+++ b/meme_chip.xml	Mon Apr 16 11:27:00 2018 -0400
@@ -1,90 +1,86 @@
-<tool id="meme_chip" name="MEME-ChIP" version="4.12.0">
+<tool id="meme_chip" name="MEME-ChIP" version="4.11.2">
     <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <code file="get_meme_motif_databases.py" />
     <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 $input
+meme-chip '$input'
 -noecho
-#if str($control) not in ['', 'None']:
+#if str($control):
     -neg '$control'
 #end if
-#if $sequence_alphabet == 'dna':
-    -dna
-#else:
-    -rna
-#end if
 -o '$output.files_path'
 #if str($options_type)=='advanced':
-    #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
-    ## FIXME: CentriMo cannot be run,  See the comments in the input tag section.
+    ## 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) == "true":
+    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_local):
     ##         -centrimo-local
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_score) != "0":
+    ##     #if str($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) != "0":
+    ##     #if str($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) != "0":
+    ##     #if str($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) == "true":
+    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_noseq):
     ##         -centrimo-noseq
     ##     #end if
-    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_flip) == "true":
+    ##     #if str($options_type_cond.run_centrimo_cond.centrimo_flip):
     ##         -centrimo-flip
     ##     #end if
     ## #end if
-    #if str($options_type_cond.search_given_strand) == "true":
+    #if str($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) != "0":
+        #if str($seed):
             -seed $options_type_cond.subsampling_cond.subsampling.seed
         #end if
     #end if
-    #if str($options_type_cond.nmeme) != "0":
+    #if str($options_type_cond.nmeme):
         -nmeme $options_type_cond.nmeme
     #end if
-    #if str($options_type_cond.ccut) != "0":
+    #if str($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) != "0":
+    #if str($options_type_cond.group_weak):
         -group-weak $options_type_cond.group_weak
     #end if
-    -filter-thresh $options_type_cond.filter_threash
-    #if str($options_type_cond.old_clustering) == "true":
+    -filter-thresh $options_type_cond.filter_thresh
+    #if str($options_type_cond.old_clustering):
         -old-clustering
     #end if
     -meme-mod $options_type_cond.meme_mod
-    #if str($options_type_cond.meme_minw) != "0":
+    #if str($options_type_cond.meme_minw):
         -meme-minw $options_type_cond.meme_minw
     #end if
-    #if str($options_type_cond.meme_maxw) != "0":
+    #if str($options_type_cond.meme_maxw):
         -meme-maxw $options_type_cond.meme_maxw
     #end if
-    #if str($options_type_cond.meme_nmotifs) != '0':
+    #if str($options_type_cond.meme_nmotifs):
         -meme-nmotifs $options_type_cond.meme_nmotifs
     #end if
-    #if str($options_type_cond.meme_minsites) != "0":
+    #if str($options_type_cond.meme_minsites):
         -meme-minsites $options_type_cond.meme_minsites
     #end if
-    #if str($options_type_cond.meme_maxsites) != "0":
+    #if str($options_type_cond.meme_maxsites):
         -meme-maxsites $options_type_cond.meme_maxsites
     #end if
-    #if str($options_type_cond.meme_pal) == "true":
+    #if str($options_type_cond.meme_pal):
         -meme-pal
     #end if
     -dreme-e $options_type_cond.dreme_e
@@ -92,11 +88,6 @@
     -spamo-skip
     -fimo-skip
 #end if
-&>meme_chip_log.txt;
-if [[ $? -ne 0 ]]; then
-    cp meme_chip_log.txt '$output';
-    exit 1;
-fi
 && rm '$output'
 && ln -s $primary_output '$output'
     ]]></command>
@@ -104,8 +95,8 @@
         <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
         <param name="control" type="data" format="fasta" optional="true" label="Control sequences" help="If no selection, positive sequences in the input are shuffled to create the negative set"/>
         <param name="sequence_alphabet" type="select" label="Sequence alphabet">
-            <option value="dna" selected="true">DNA</option>
-            <option value="rna">RNA</option>
+            <option value="-dna" selected="true">DNA</option>
+            <option value="-rna">RNA</option>
         </param>
         <conditional name="options_type_cond">
             <param name="options_type" type="select" label="Options Configuration">
@@ -137,9 +128,9 @@
                         </param>
                         <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/>
                         <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/>
-                        <param name="centrimo_score" type="integer" value="0" min="0" label="Minimum allowed CentriMo match score"/>
-                        <param name="centrimo_maxreg" type="integer" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
-                        <param name="centrimo_ethresh" type="integer" value="0" min="0" label="CentriMo E-value threshold for reporting" />
+                        <param name="centrimo_score" type="integer" optional="true" value="0" min="0" label="Minimum allowed CentriMo match score"/>
+                        <param name="centrimo_maxreg" type="integer" optional="true" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
+                        <param name="centrimo_ethresh" type="integer" optional="true" value="0" min="0" label="CentriMo E-value threshold for reporting" />
                         <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
                         <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
                     </when>
@@ -153,20 +144,20 @@
                     <option value="3">3rd order model of sequences</option>
                     <option value="4">4th order model of sequences</option>
                 </param>
-                <param name="nmeme" type="integer" 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="0" min="0" label="Limit of sequences to pass to MEME" help="Zero value has no effect"/>
                 <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" 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="0" min="0" label="Seed for the randomized selection of sequences" help="Zero value indicates random seeding"/>
                     </when>
                     <when value="no"/>
                 </conditional>
-                <param name="ccut" type="integer" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/>
+                <param name="ccut" type="integer" optional="true" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/>
                 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
-                <param name="group_weak" type="float" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
+                <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"/>
@@ -175,11 +166,11 @@
                     <option value="zoops">Zero or one occurances per sequence</option>
                     <option value="anr">Any number of repititions</option>
                 </param>
-                <param name="meme_minw" type="integer" value="0" min="0" label="Minimum motif width"/>
-                <param name="meme_maxw" type="integer" value="0" min="0" label="Maximum motif width"/>
-                <param name="meme_nmotifs" type="integer" value="0" min="0" label="Maximum number of motifs to find"/>
-                <param name="meme_minsites" type="integer" value="0" min="0" label="Minimum number of sites per motif"/>
-                <param name="meme_maxsites" type="integer" value="0" label="Maximum number of sites per motif"/>
+                <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/>
+                <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/>
+                <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 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" />
@@ -194,8 +185,17 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="extract_genomic_dna.fa" ftype="fasta"/>
-            <output name="output" file="sample_output.html" ftype="html"/>
+            <param name="input" value="input1.fasta" ftype="fasta"/>
+            <param name="non_commercial_use" value="True"/>
+            <output name="output" file="output1.html" ftype="html" compare="contains"/>
+        </test>
+        <test>
+            <param name="input" value="input1.fasta" ftype="fasta"/>
+            <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"/>
+            <output name="output" file="output1.html" ftype="html" compare="contains"/>
         </test>
     </tests>
     <help>