--- a/augustus.xml	Fri Dec 20 14:08:53 2019 -0500
+++ b/augustus.xml	Thu Jul 15 17:16:12 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@">
+<tool id="augustus" name="Augustus" profile="20.01" version="@VERSION@+galaxy@SUFFIX_VERSION@">
     <description>gene prediction for prokaryotic and eukaryotic genomes</description>
     <macros>
         <import>macros.xml</import>
@@ -68,7 +68,7 @@
             $input_genome
             $utr
             --genemodel=$genemodel
-
+            --softmasking=$softmasking
             #if $hints.usehints == 'T'
                 --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
             #end if
@@ -125,11 +125,13 @@
                     <!-- 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</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>
@@ -183,13 +185,13 @@
                     <option value="cacao">Theobroma cacao (cacao)</option>
                     <option value="heliconius_melpomene1">Heliconius melpomene</option>
                     <option value="xenoturbella">Xenoturbella</option>
-                    <option value="E_coli_K12">E coli K12</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">wheat</option>
+                    <option value="wheat">Triticum aestivum</option>
                     <option value="zebrafish">Danio rerio</option>
                     <option value="anidulans">Aspergillus nidulans</option>
                     <option value="bombus_impatiens1">Bombus impatiens1</option>
@@ -205,23 +207,55 @@
                     <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>
-                    <option value="adorsata">adorsata</option>
-                    <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
-                    <option value="maker2_athal1">maker2_athal1</option>
-                    <option value="maker2_c_elegans1">maker2_c_elegans1</option>
-                    <option value="maker2_dmel1">maker2_dmel1</option>
-                    <option value="maker2_spomb1">maker2_spomb1</option>
-                    <option value="parasteatoda">parasteatoda</option>
-                    <option value="rice">rice</option>
-                    <option value="schistosoma2">schistosoma2</option>
-                    <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</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="Encephalitozoon_cuniculi">Encephalitozoon cuniculi</option>
+                    <option value="Gonapodya_prolifera">Dunaliella salina</option>
+                    <option value="Sordaria_macrospora">Sordaria macrospora</option>
+                    <option value="Sphaceloma_murrayae">Sphaceloma murrayae</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>
                 </param>
             </when>
         </conditional>
 
+        <param name="softmasking" 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 name="strand" type="select" argument="--strand"
             label="Predict genes on specific strands">
             <option value="both">both</option>
@@ -299,6 +333,7 @@
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <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>
@@ -306,12 +341,14 @@
             <param name="organism" value="human" />
             <param name="utr" value="True" />
             <param name="gff" value="True" />
+            <param name="softmasking" value="False"/>
             <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/>
         </test>
         <test>
             <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <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"/>
             <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
             <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
@@ -323,6 +360,7 @@
             <param name="hintsfile" value="hints.truncated.adjusted.gff" />
             <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
             <param name="outputs" value="" />
+            <param name="softmasking" value="False"/>
             <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
                 <assert_contents>
                     <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
@@ -341,6 +379,7 @@
             <param name="start" value="7000" />
             <param name="stop" value="9000" />
             <param name="outputs" value="" />
+            <param name="softmasking" value="False"/>
             <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" />
@@ -348,6 +387,14 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test softmasking parameter-->
+        <test>
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
+            <param name="organism" value="human" />
+            <param name="utr" value="True" />
+            <param name="softmasking" value="True"/>
+            <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
+        </test>
 
     </tests>
     <help>