--- a/augustus.xml	Sun Dec 15 09:09:57 2024 +0000
+++ b/augustus.xml	Thu Jul 17 09:06:01 2025 +0000
@@ -13,13 +13,13 @@
 
             ## Using an augustus model from history, we need to unzip it and let augustus find it
 
-            cp -r `command -v augustus | xargs dirname`/../config/ augustus_dir/ &&
+            cp -r \$(dirname \$(command -v augustus))/../config/ augustus_dir/ &&
 
             mkdir -p 'augustus_dir/species/' &&
 
-            tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /dev/null &&
+            tar -C 'augustus_dir/species/' -xzvf '$model.custom_model' > /dev/null &&
 
-            export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+            export AUGUSTUS_CONFIG_PATH=./augustus_dir/ &&
         #end if
 
         ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
@@ -31,44 +31,15 @@
             $gff
             --uniqueGeneId=true
 
-            #if 'protein' in str($outputs).split(','):
-                --protein=on
-            #else:
-                --protein=off
-            #end if
-
-            #if 'codingseq' in str($outputs).split(','):
-                --codingseq=on
-            #else:
-                --codingseq=off
-            #end if
-
-            #if 'introns' in str($outputs).split(','):
-                --introns=on
-            #else:
-                --introns=off
-            #end if
-
-            #if 'start' in str($outputs).split(','):
-                --start=on
-            #else:
-                --stop=off
-            #end if
-
-            #if 'stop' in str($outputs).split(','):
-                --stop=on
-            #else:
-                --stop=off
-            #end if
-
-            #if 'cds' in str($outputs).split(','):
-                --cds=on
-            #else:
-                --cds=off
-            #end if
-
+            #for arg in ['protein', 'codingseq', 'introns', 'start', 'stop', 'cds']
+                #if arg in $outputs:
+                    --$arg=on
+                #else
+                    --$arg=off 
+                #end if
+            #end for
             $singlestrand
-            $input_genome
+            '$input_genome'
             $utr
             --genemodel=$genemodel
             --softmasking=$softmasking
@@ -99,7 +70,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
+        <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genome Sequence"/>
         <param argument="--noInFrameStop" type="boolean"
             label="Don't report transcripts with in-frame stop codons"
             truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false"
@@ -124,145 +95,185 @@
                 <param name="custom_model" argument="--species" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/>
             </when>
             <when value="builtin">
-                <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="txt" help="Choose a specialised trainingset.">
+                <param name="organism" argument="--species" label="Model Organism" type="select" multiple="false" format="txt" help="Choose a specialised trainingset. If model name is different than species name it is shown in parentheses." >
                     <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) -->
-                    <option value="human">Homo sapiens</option>
-                    <option value="fly">Drosophila melanogaster</option>
-                    <option value="maker2_dmel1">Drosophila melanogaster (maker2_dmel1)</option>
-                    <option value="arabidopsis">Arabidopsis thaliana</option>
-                    <option value="brugia">Brugia malayi (brugia)</option>
-                    <option value="brugia_malayi">Brugia malayi (brugia_malayi)</option>
-                    <option value="aedes">Aedes aegypti</option>
-                    <option value="tribolium2012">Tribolium castaneum</option>
-                    <option value="schistosoma">Schistosoma mansoni</option>
-                    <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
-                    <option value="tetrahymena">Tetrahymena thermophila</option>
-                    <option value="galdieria">Galdieria sulphuraria</option>
-                    <option value="maize">Zea mays</option>
-                    <option value="toxoplasma">Toxoplasma gondii</option>
-                    <option value="caenorhabditis">Caenorhabditis elegans</option>
+                    <!-- Current list for AUGUSTUS (3.5.0) for i in $(ls ~/miniforge3/envs/__busco@5.8.0/config/species/); do echo \<option value=\"$i\"\>$(echo $i | sed 's/_/ /g')\</option\>; done -->
+                    <option value="adorsata">Apis dorsata (adorsata)</option>
+                    <option value="aedes">Aedes aegypti (aedes)</option>
+                    <option value="amphimedon">Amphimedon queenslandica</option>
+                    <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
+                    <option value="anidulans">Aspergillus nidulans (anidulans)</option>
+                    <option value="Anopheles_gambiae">Anopheles gambiae</option>
+                    <option value="arabidopsis">Arabidopsis thaliana (arabidopsis)</option>
+                    <option value="Argopecten_irradians">Argopecten irradians</option>
                     <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
-                    <option value="anidulans">Aspergillus nidulans (anidulans)</option>
-                    <option value="aspergillus_nidulans">Aspergillus nidulans (aspergillus_nidulans)</option>
+                    <option value="aspergillus_nidulans">Aspergillus nidulans</option>
                     <option value="aspergillus_oryzae">Aspergillus oryzae</option>
                     <option value="aspergillus_terreus">Aspergillus terreus</option>
+                    <option value="Aurelia_aurita">Aurelia aurita</option>
+                    <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
+                    <option value="Berviolum_minutum">Berviolum minutum</option>
+                    <option value="bombus_impatiens1">Bombus impatiens1</option>
+                    <option value="bombus_terrestris2">Bombus terrestris2</option>
                     <option value="botrytis_cinerea">Botrytis cinerea</option>
+                    <option value="b_pseudomallei">Burkholderia pseudomallei (b_pseudomallei)</option>
+                    <option value="Branchiostoma_floridae">Branchiostoma floridae</option>
+                    <option value="brugia">Brugia malayi (brugia)</option>
+                    <option value="cacao">(cacao)</option>
+                    <option value="caenorhabditis">Caenorhabditis elegans (caenorhabditis)</option>
+                    <option value="camponotus_floridanus">Camponotus floridanus</option>
                     <option value="candida_albicans">Candida albicans</option>
                     <option value="candida_guilliermondii">Candida guilliermondii</option>
                     <option value="candida_tropicalis">Candida tropicalis</option>
+                    <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
+                    <!-- <option value="c_elegans_trsk">Caenorhabditis elegans</option> do not use according to augustus commit messages -->
                     <option value="chaetomium_globosum">Chaetomium globosum</option>
+                    <option value="chicken">Gallus gallus (chicken)</option>
+                    <option value="chiloscyllium">Chiloscyllium punctatum (chiloscyllium)</option>
+                    <option value="chlamy2011">chlamy2011</option>
+                    <option value="chlamydomonas">Chlamydomonas reinhardtii (chlamydomonas)</option>
+                    <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
+                    <option value="chlorella">chlorella</option>
+                    <option value="Chloropicon_primus">Chloropicon primus</option>
+                    <option value="Chrysaora_chesapeakei">Chrysaora chesapeakei</option>
+                    <option value="ciona">ciona</option>
                     <option value="coccidioides_immitis">Coccidioides immitis</option>
-                    <option value="coprinus">Coprinus cinereus (coprinus)</option>
-                    <option value="coprinus_cinereus">Coprinus cinereus (coprinus_cinereus)</option>
+                    <option value="Conidiobolus_coronatus">Conidiobolus coronatus</option>
+                    <option value="coprinus">coprinus</option>
+                    <option value="coprinus_cinereus">Coprinus cinereus</option>
+                    <option value="coyote_tobacco">Coyote tobacco</option>
+                    <option value="cryptococcus">cryptococcus</option>
                     <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</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="cryptococcus">Cryptococcus neoformans (cryptococcus)</option>
-                    <option value="cryptococcus_neoformans">Cryptococcus neoformans (cryptococcus_neoformans)</option>
+                    <option value="Cryptosporidium_hominis">Cryptosporidium hominis</option>
+                    <option value="culex">culex</option>
+                    <option value="Cyclotella_cryptica">Cyclotella cryptica</option>
                     <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
+                    <option value="Dermasterias_imbricata">Dermasterias imbricata</option>
+                    <option value="Dunaliella_salina">Dunaliella salina</option>
+                    <option value="E_coli_K12">Escherichia K12 (E_coli_K12)</option>
+                    <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
+                    <option value="elephant_shark">Callorhinchus milii (elephant_shark)</option>
                     <option value="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
                     <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi GB</option>
                     <option value="eremothecium_gossypii">Eremothecium gossypii</option>
+                    <option value="Fistulifera_solaris">Fistulifera solaris</option>
+                    <option value="fly">Drosophila melanogaster (fly)</option>
+                    <option value="fly_exp">Drosophila melanogaster (fly) experimental parameters</option>
+                    <option value="Fragilariopsis_cylindrus_CCMP1102">Fragilariopsis cylindrus CCMP1102</option>
+                    <option value="fusarium">fusarium</option>
                     <option value="fusarium_graminearum">Fusarium graminearum</option>
-                    <option value="histoplasma_capsulatum">Histoplasma capsulatum (histoplasma_capsulatum)</option>
-                    <option value="histoplasma">Histoplasma capsulatum (histoplasma)</option>
+                    <option value="galdieria">Galdieria sulphuraria (galdieria)</option>
+                    <option value="generic">generic</option>
+                    <option value="gigaspora_margarita">Gigaspora margarita</option>
+                    <option value="Gonapodya_prolifera">Gonapodya prolifera</option>
+                    <option value="heliconius_melpomene1">Heliconius melpomene1</option>
+                    <option value="histoplasma">histoplasma</option>
+                    <option value="histoplasma_capsulatum">Histoplasma capsulatum</option>
+                    <option value="honeybee1">Apis mellifera (honeybee1)</option>
+                    <option value="human">Homo sapiens (human)</option>
+                    <option value="Hydra_vulgaris">Hydra vulgaris</option>
+                    <option value="hymenolepis_microstoma">Hymenolepis microstoma</option>
+                    <option value="japaneselamprey">Lethenteron camtschaticum (japaneselamprey)</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="Leptasterias_sp">Leptasterias sp</option>
+                    <option value="Loa_loa">Loa loa</option>
                     <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
                     <option value="magnaporthe_grisea">Magnaporthe grisea</option>
+                    <option value="maize">Zea mays (maize)</option>
+                    <option value="maize5">Zea mays (maize5)</option>
+                    <option value="Micromonas_commoda">Micromonas commoda</option>
+                    <option value="Micromonas_pusilla">Micromonas pusilla</option>
+                    <option value="mnemiopsis_leidyi">Mnemiopsis leidyi</option>
+                    <option value="Monoraphidium_neglectum">Monoraphidium neglectum</option>
+                    <option value="Monosiga_brevicollis">Monosiga brevicollis</option>
+                    <option value="Naegleria_gruberi">Naegleria gruberi</option>
+                    <option value="nasonia">Nasonia vitripennis (nasonia)</option>
+                    <option value="nematostella_vectensis">Nematostella vectensis</option>
+                    <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
+                    <option value="neurospora">neurospora</option>
                     <option value="neurospora_crassa">Neurospora crassa</option>
+                    <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
+                    <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp lucimarinus</option>
+                    <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
+                    <option value="Paramecium_tetraurelia">Paramecium tetraurelia</option>
+                    <option value="parasteatoda">Parasteatoda tepidariorum (parasteatoda)</option>
+                    <option value="pchrysosporium">Phanerochaete chrysosporium (pchrysosporium)</option>
+                    <option value="pea_aphid">Acyrthosiphon pisum (pea_aphid)</option>
+                    <option value="Pediculus_humanus">Pediculus humanus</option>
+                    <option value="Perkinsus_marinus">Perkinsus marinus</option>
+                    <option value="pfalciparum">Plasmodium falciparum (pfalciparum)</option>
+                    <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
                     <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
+                    <option value="Physcomitrium_patens">Physcomitrium patens</option>
                     <option value="pichia_stipitis">Pichia stipitis</option>
+                    <option value="pisaster">Pisaster ochraceus (pisaster)</option>
+                    <option value="pneumocystis">pneumocystis</option>
+                    <option value="Populus_trichocarpa">Populus trichocarpa</option>
+                    <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
+                    <option value="Ptychodera_flava">Ptychodera flava</option>
+                    <option value="Pycnopodia_helianthoides">Pycnopodia helianthoides</option>
+                    <option value="Raphidocelis_subcapitata">Raphidocelis subcapitata</option>
+                    <option value="rhincodon">Rhincodon typus (rhincodon)</option>
                     <option value="rhizopus_oryzae">Rhizopus oryzae</option>
-                    <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae saccharomyces_cerevisiae_S288C</option>
-                    <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae RM11-1a-1</option>
-                    <option value="saccharomyces">Saccharomyces cerevisiae (saccharomyces)</option>
+                    <option value="rhodnius">Rhodnius</option>
+                    <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
+                    <option value="rice">Oryza (rice)</option>
+                    <option value="Ricinus_communis">Ricinus communis</option>
+                    <option value="saccharomyces">Saccharomyces</option>
+                    <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a 1</option>
+                    <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option>
+                    <option value="s_aureus">Staphylococcus aureus (s_aureus)</option>
+                    <option value="schistosoma">Schistosoma mansoni (schistosoma)</option>
+                    <option value="schistosoma2">Schistosoma mansoni (schistosoma2)</option>
                     <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
-                    <option value="trichinella">Trichinella spiralis</option>
-                    <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
-                    <option value="nasonia">Nasonia vitripennis</option>
-                    <option value="tomato">Solanum lycopersicum</option>
-                    <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
-                    <option value="amphimedon">Amphimedon queenslandica</option>
-                    <option value="pneumocystis">Pneumocystis jirovecii</option>
-                    <option value="chicken">Gallus gallus domesticus (chicken)</option>
-                    <option value="cacao">Theobroma cacao (cacao)</option>
-                    <option value="heliconius_melpomene1">Heliconius melpomene</option>
-                    <option value="xenoturbella">Xenoturbella</option>
-                    <option value="E_coli_K12">Escherichia coli K12</option>
-                    <option value="c_elegans_trsk">c elegans trsk</option>
-                    <option value="camponotus_floridanus">Camponotus floridanus</option>
-                    <option value="coyote_tobacco">Coyote tobacco</option>
-                    <option value="s_aureus">Staphylococcus aureus</option>
-                    <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
-                    <option value="wheat">Triticum aestivum</option>
-                    <option value="zebrafish">Danio rerio</option>
-                    <option value="bombus_impatiens1">Bombus impatiens1</option>
-                    <option value="bombus_terrestris2">Bombus terrestris2</option>
-                    <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
-                    <option value="culex_pipiens">Culex pipiens</option>
-                    <option value="elephant_shark">Callorhinchus milii</option>
-                    <option value="honeybee1">Apis mellifera</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-atrum</option>
-                    <option value="verticillium_longisporum1">Verticillium longisporum</option>
-                    <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
-                    <option value="adorsata">Apis dorsata</option>
-                    <option value="ancylostoma_ceylanicum">Ancylostoma ceylanicum</option>
-                    <option value="maker2_athal1">Arabidopsis thaliana (maker2_athal1)</option>
-                    <option value="maker2_c_elegans1">Caenorhabditis elegans (maker2_c_elegans1)</option>
-                    <option value="maker2_spomb1">Saccharomyces cerevisiae (maker2_spomb1)</option>
-                    <option value="parasteatoda">Parasteatoda SP.</option>
-                    <option value="rice">Oryza sp.</option>
-                    <option value="Cassiopea_xamachana">Cassiopea xamachana</option>
-                    <option value="Ptychodera_flava">Ptychodera flava</option>
-                    <option value="Argopecten_irridians">Argopecten irridians</option>
-                    <option value="Nemopilema_nomurai">Nemopilema nomurai</option>
-                    <option value="Notospermus_geniculatus">Notospermus geniculatus</option>
-                    <option value="Chrysaora_chesapeakeij">Chrysaora chesapeakeij</option>
-                    <option value="Ectocarpus_siliculosus">Ectocarpus siliculosus</option>
-                    <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
-                    <option value="Aurelia_aurita">Aurelia aurita</option>
-                    <option value="Rhopilema_esculentum">Rhopilema esculentum</option>
-                    <option value="Gonapodya_prolifera">Dunaliella salina</option>
+                    <option value="Sclerotinia_sclerotiorum">Sclerotinia sclerotiorum</option>
+                    <option value="scyliorhinus">Scyliorhinus torazame (scyliorhinus)</option>
+                    <option value="sealamprey">Petromyzon marinus (sealamprey)</option>
+                    <option value="Skeletonema_costatum">Skeletonema costatum</option>
                     <option value="Sordaria_macrospora">Sordaria macrospora</option>
                     <option value="Sphaceloma_murrayae">Sphaceloma murrayae</option>
+                    <option value="s_pneumoniae">Streptococcus pneumoniae (s_pneumoniae)</option>
+                    <option value="strongylocentrotus_purpuratus">Strongylocentrotus purpuratus</option>
+                    <option value="sulfolobus_solfataricus">Sulfolobus solfataricus</option>
+                    <option value="sunflower">Helianthus annuus (sunflower)</option>
+                    <option value="Taeniopygia_guttata">Taeniopygia guttata</option>
+                    <option value="template_prokaryotic">Template prokaryotic</option>
+                    <option value="tetrahymena">tetrahymena</option>
+                    <option value="Thalassiosira_pseudonana_CCMP1335">Thalassiosira pseudonana CCMP1335</option>
+                    <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
+                    <option value="tomato">Solanum lycopersicum (tomato)</option>
+                    <option value="toxoplasma">Toxoplasma gondii (toxoplasma)</option>
+                    <option value="tribolium2012">tribolium2012</option>
+                    <option value="trichinella">Trichinella</option>
+                    <option value="Trichoplax_adhaerens">Trichoplax adhaerens</option>
+                    <option value="Trypanosoma_cruzi">Trypanosoma cruzi</option>
+                    <option value="ustilago">Ustilago</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="Vitis_vinifera">Vitis vinifera</option>
                     <option value="Vitrella_brassicaformis">Vitrella brassicaformis</option>
-                    <option value="Monoraphidium_neglectum">Monoraphidium_neglectum</option>
-                    <option value="Raphidocelis_subcapita">Raphidocelis subcapita</option>
-                    <option value="Ostreococcus_tauri">Ostreococcus tauri</option>
-                    <option value="Ostreococcus_sp_lucimarinus">Ostreococcus sp. lucimarinus</option>
-                    <option value="Micromonas_pusilla">Micromonas pusilla</option>
-                    <option value="Micromonas_commoda">Micromonas commoda</option>
-                    <option value="Chlamydomonas_eustigma">Chlamydomonas eustigma</option>
-                    <option value="Thalassiosira_pseudonana">Thalassiosira pseudonana</option>
-                    <option value="Pseudo-nitzschia_multistriata">Pseudo-nitzschia multistriata</option>
-                    <option value="Phaeodactylum_tricornutum">Phaeodactylum tricornutum</option>
-                    <option value="Fragilariopsis_cylindrus">Fragilariopsis cylindrus</option>
-                    <option value="Fistulifera_solaris">Fistulifera solaris</option>
-                    <option value="Bathycoccus_prasinos">Bathycoccus prasinos</option>
-                    <option value="Chloropicon_primus">Chloropicon primus</option>
+                    <option value="volvox">volvox</option>
+                    <option value="wheat">wheat</option>
+                    <option value="Xenopus_tropicalis">Xenopus tropicalis</option>
+                    <option value="Xiphophorus_maculatus">Xiphophorus maculatus</option>
+                    <option value="Xipophorus_maculatus">Xipophorus maculatus</option>
+                    <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
+                    <option value="zebrafish">Danio rerio (zebrafish)</option>
                 </param>
             </when>
         </conditional>
 
-        <param type="boolean" argument="--softmasking"
-        label="Softmasking"
-        truevalue="1" falsevalue="0" checked="true"
-        help="If this option is enabled, lowercase letters are considered as repeated regions." />
-
-
-        <param type="select" argument="--strand"
-            label="Predict genes on specific strands">
+        <param type="boolean" argument="--softmasking" label="Softmasking" truevalue="1" falsevalue="0" checked="true" help="If this option is enabled, lowercase letters are considered as repeated regions." />
+        <param type="select" argument="--strand" label="Predict genes on specific strands">
             <option value="both">both</option>
             <option value="forward">forward</option>
             <option value="backward">backward</option>
         </param>
-
         <param argument="--genemodel" label="Gene Model" type="select"
             help="Gene Model to predict, for more information please refer to the help.">
             <option value="complete">complete</option>
@@ -271,7 +282,6 @@
             <option value="atleastone">atleastone</option>
             <option value="exactlyone">exactlyone</option>
         </param>
-
         <conditional name="hints">
             <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
                 <option value="F">No</option>
@@ -286,7 +296,6 @@
             <when value="F">
             </when>
     	</conditional>
-
         <conditional name="range">
             <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
                 <option value="F">No</option>
@@ -301,14 +310,10 @@
             <when value="F">
             </when>
         </conditional>
-
-        <param name="gff" argument="--gff3" type="boolean" label="GFF formated output"
-            help="Standard output is GTF."
-            truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
-
-        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
-            <option value="protein" selected="True">predicted protein sequences (--protein)</option>
-            <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option>
+        <param name="gff" argument="--gff3" type="boolean" label="GFF formated output" help="Standard output is GTF." truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />
+        <param name="outputs" type="select" optional="true" multiple="true" label="Output options">
+            <option value="protein" selected="true">predicted protein sequences (--protein)</option>
+            <option value="codingseq" selected="true">coding sequence as comment in the output file (--codingseq)</option>
             <option value="introns">predicted intron sequences (--introns)</option>
             <option value="start">predicted start codons (--start)</option>
             <option value="stop">predicted stop codons (--stop)</option>
@@ -322,23 +327,27 @@
             </change_format>
         </data>
         <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
-            <filter>'protein' in outputs</filter>
+            <filter>outputs and 'protein' in outputs</filter>
         </data>
         <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
-            <filter>'codingseq' in outputs</filter>
+            <filter>outputs and 'codingseq' in outputs</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
-            <param name="organism" value="human" />
+            <param name="input_genome" value="human_augustus.fa.gz" ftype="fasta.gz" />
+            <conditional name="model">
+                <param name="organism" value="human" />
+            </conditional>
             <param name="utr" value="True" />
             <param name="softmasking" value="False"/>
             <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
-            <param name="organism" value="human" />
+            <conditional name="model">
+                <param name="organism" value="human" />
+            </conditional>
             <param name="utr" value="True" />
             <param name="gff" value="True" />
             <param name="softmasking" value="False"/>
@@ -346,7 +355,9 @@
         </test>
         <test expect_num_outputs="3">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
-            <param name="organism" value="human" />
+            <conditional name="model">
+                <param name="organism" value="human" />
+            </conditional>
             <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
             <param name="softmasking" value="False"/>
             <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
@@ -355,11 +366,15 @@
         </test>
         <test expect_num_outputs="1">
             <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
-            <param name="organism" value="fly" />
-            <param name="usehints" value="T" />
-            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
-            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
-            <param name="outputs" value="" />
+            <conditional name="model">
+                <param name="organism" value="fly" />
+            </conditional>
+            <conditional name="hints">
+                <param name="usehints" value="T" />
+                <param name="hintsfile" value="hints.truncated.adjusted.gff" />
+                <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
+            </conditional>
+            <param name="outputs" value_json="null" />
             <param name="softmasking" value="False"/>
             <param name="outputs" value=""/>
             <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
@@ -372,16 +387,22 @@
         </test>
         <test expect_num_outputs="1">
             <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
-            <param name="organism" value="fly" />
-            <param name="usehints" value="T" />
-            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
-            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
-            <param name="userange" value="T" />
-            <param name="start" value="7000" />
-            <param name="stop" value="9000" />
-            <param name="outputs" value="" />
+            <conditional name="model">
+                <param name="organism" value="fly" />
+            </conditional>
+            <conditional name="hints">
+                <param name="usehints" value="T" />
+                <param name="hintsfile" value="hints.truncated.adjusted.gff" />
+                <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
+            </conditional>
+            <conditional name="range">
+                <param name="userange" value="T" />
+                <param name="start" value="7000" />
+                <param name="stop" value="9000" />
+            </conditional>
+            <param name="outputs" value_json="null" />
             <param name="softmasking" value="False"/>
-            <param name="outputs" value=""/>
+            <param name="outputs"  value_json="null"/>
             <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
                 <assert_contents>
                     <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
@@ -392,10 +413,12 @@
         <!-- Test softmasking parameter-->
         <test expect_num_outputs="1">
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
-            <param name="organism" value="human" />
+            <conditional name="model">
+                <param name="organism" value="human" />
+            </conditional>
             <param name="utr" value="True" />
             <param name="softmasking" value="True"/>
-            <param name="outputs" value=""/>
+            <param name="outputs" value_json="null"/>
             <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
         </test>