--- a/busco.xml	Tue Nov 02 09:40:29 2021 +0000
+++ b/busco.xml	Fri Nov 05 08:41:35 2021 +0000
@@ -49,7 +49,7 @@
     #end if
 #end if
 
-#if $adv.outputs and 'image' in $adv.outputs:
+#if $outputs and 'image' in $outputs:
     &&
     mkdir BUSCO_summaries
     &&
@@ -119,26 +119,27 @@
             </when>
         </conditional>
 
+        <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
+            <option value="short_summary" selected="true">short summary text</option>
+            <option value="missing">list with missing IDs</option>
+            <option value="image">summary image</option>
+        </param>
+
         <section name="adv" title="Advanced Options" expanded="False">
             <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
             <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
-            <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
-                <option value="short_summary">short summary text</option>
-                <option value="missing">list with missing IDs</option>
-                <option value="image">summary image</option>
-            </param>
         </section>
     </inputs>
     <outputs>
         <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
-            <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter>
+            <filter>outputs and 'short_summary' in outputs</filter>
         </data>
         <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
         <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
-            <filter>adv['outputs'] and 'missing' in adv['outputs']</filter>
+            <filter>outputs and 'missing' in outputs</filter>
         </data>
         <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
-            <filter>adv['outputs'] and 'image' in adv['outputs']</filter>
+            <filter>outputs and 'image' in outputs</filter>
         </data>
     </outputs>
     <tests>
@@ -154,9 +155,7 @@
                     <param name="use_augustus_selector" value="yes" />
                 </conditional>
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing" />
-            </section>
+            <param name="outputs" value="short_summary,missing" />
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
@@ -174,9 +173,7 @@
             <conditional name="busco_mode">
                 <param name="mode" value="prot" />
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing,image" />
-            </section>
+            <param name="outputs" value="short_summary,missing,image" />
             <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
@@ -191,9 +188,7 @@
             <conditional name="busco_mode">
                 <param name="mode" value="tran" />
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing,image" />
-            </section>
+            <param name="outputs" value="short_summary,missing,image" />
             <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
             <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
@@ -215,9 +210,7 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary" />
-            </section>
+            <param name="outputs" value="short_summary" />
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
         </test>
@@ -237,9 +230,7 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing" />
-            </section>
+            <param name="outputs" value="short_summary,missing" />
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
@@ -256,9 +247,7 @@
                     <param name="use_augustus_selector" value="no" />
                 </conditional>
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing,image" />
-            </section>
+            <param name="outputs" value="short_summary,missing,image" />
             <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
             <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
@@ -276,9 +265,7 @@
                     <param name="use_augustus_selector" value="no" />
                 </conditional>
             </conditional>
-            <section name="adv">
-                <param name="outputs" value="short_summary,missing,image" />
-            </section>
+            <param name="outputs" value="short_summary,missing,image" />
             <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" />
             <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" />