# HG changeset patch
# User iuc
# Date 1636101695 0
# Node ID 46ae58b1d7926aac3448323e6f7a178c60afcd06
# Parent  1278204240d830f6fbeb66f155fff0bcd15c8962
"planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"

diff -r 1278204240d8 -r 46ae58b1d792 busco.xml
--- 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" />
diff -r 1278204240d8 -r 46ae58b1d792 macros.xml
--- a/macros.xml	Tue Nov 02 09:40:29 2021 +0000
+++ b/macros.xml	Fri Nov 05 08:41:35 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">5.2.2</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
 
     <xml name="citations">
         <citations>
@@ -14,7 +14,6 @@
         <option value="human">Homo sapiens</option>
         <option value="fly">Drosophila melanogaster</option>
         <option value="arabidopsis">Arabidopsis thaliana</option>
-        <option value="brugia ">Brugia malayi</option>
         <option value="aedes">Aedes aegypti</option>
         <option value="tribolium2012">Tribolium castaneum</option>
         <option value="schistosoma">Schistosoma mansoni</option>
@@ -22,41 +21,38 @@
         <option value="galdieria">Galdieria sulphuraria</option>
         <option value="maize">Zea mays</option>
         <option value="toxoplasma">Toxoplasma gondii</option>
-        <option value="caenorhabditis ">Caenorhabditis elegans</option>
+        <option value="caenorhabditis">Caenorhabditis elegans</option>
         <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
-        <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
-        <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
+        <option value="aspergillus_nidulans">Aspergillus nidulans</option>
+        <option value="aspergillus_oryzae">Aspergillus oryzae</option>
         <option value="aspergillus_terreus">Aspergillus terreus</option>
-        <option value="botrytis_cinerea ">Botrytis cinerea</option>
-        <option value="candida_albicans ">Candida albicans</option>
-        <option value="candida_guilliermondii ">Candida guilliermondii</option>
-        <option value="candida_tropicalis ">Candida tropicalis</option>
+        <option value="botrytis_cinerea">Botrytis cinerea</option>
+        <option value="candida_albicans">Candida albicans</option>
+        <option value="candida_guilliermondii">Candida guilliermondii</option>
+        <option value="candida_tropicalis">Candida tropicalis</option>
         <option value="chaetomium_globosum">Chaetomium globosum</option>
         <option value="coccidioides_immitis">Coccidioides immitis</option>
-        <option value="coprinus">Coprinus cinereus</option>
         <option value="coprinus_cinereus">Coprinus cinereus</option>
         <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
-        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
-        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
-        <option value="cryptococcus">Cryptococcus neoformans</option>
+        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option>
+        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option>
         <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
         <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
         <option value="eremothecium_gossypii">Eremothecium gossypii</option>
-        <option value="fusarium_graminearum ">Fusarium graminearum</option>
-        <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
-        <option value="histoplasma">Histoplasma capsulatum</option>
-        <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
-        <option value="laccaria_bicolor ">Laccaria bicolor</option>
+        <option value="fusarium_graminearum">Fusarium graminearum</option>
+        <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
+        <option value="kluyveromyces_lactis">Kluyveromyces lactis</option>
+        <option value="laccaria_bicolor">Laccaria bicolor</option>
         <option value="lamprey">Petromyzon marinus</option>
         <option value="leishmania_tarentolae">Leishmania tarentolae</option>
         <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
-        <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
+        <option value="magnaporthe_grisea">Magnaporthe grisea</option>
         <option value="neurospora_crassa">Neurospora crassa</option>
         <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
         <option value="pichia_stipitis">Pichia stipitis</option>
         <option value="rhizopus_oryzae">Rhizopus oryzae</option>
-        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
-        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
+        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
+        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a_1</option>
         <option value="saccharomyces">Saccharomyces cerevisiae</option>
         <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
         <option value="trichinella">Trichinella spiralis</option>
@@ -79,20 +75,16 @@
         <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
         <option value="wheat">wheat</option>
         <option value="zebrafish">Danio rerio</option>
-        <option value="anidulans">Aspergillus nidulans</option>
         <option value="bombus_impatiens1">Bombus impatiens1</option>
         <option value="bombus_terrestris2">Bombus terrestris2</option>
-        <option value="botrytis_cinerea">Botrytis cinerea</option>
         <option value="brugia_malayi">Brugia malayi</option>
         <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
         <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
         <option value="culex_pipiens">Culex pipiens</option>
         <option value="elephant_shark">Callorhinchus milii</option>
         <option value="honeybee1">Apis mellifera</option>
-        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
         <option value="pea_aphid">Acyrthosiphon pisum</option>
         <option value="rhodnius_prolixus">Rhodnius prolixus</option>
-        <option value="ustilago_maydis">Ustilago maydis</option>
         <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
         <option value="verticillium_longisporum1">Verticillium longisporum1</option>
         <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>