<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.8.9</token>
    <token name="@VERSION_SUFFIX@">1</token>

    <xml name="requirements">
        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.5281/zenodo.4054262</citation>
        </citations>
    </xml>

    <xml name="augustus_species">
        <!-- list generated from a Funannotate database directory, listing trained_species/* -->
        <option value="adorsata">adorsata</option>
        <option value="aedes">aedes</option>
        <option value="amphimedon">amphimedon</option>
        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
        <option value="anidulans">anidulans</option>
        <option value="arabidopsis">arabidopsis</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_terreus">aspergillus_terreus</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">b_pseudomallei</option>
        <option value="brugia">brugia</option>
        <option value="cacao">cacao</option>
        <option value="caenorhabditis">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="c_elegans_trsk">c_elegans_trsk</option>
        <option value="chaetomium_globosum">chaetomium_globosum</option>
        <option value="chicken">chicken</option>
        <option value="chiloscyllium">chiloscyllium</option>
        <option value="chlamy2011">chlamy2011</option>
        <option value="chlamydomonas">chlamydomonas</option>
        <option value="chlorella">chlorella</option>
        <option value="ciona">ciona</option>
        <option value="coccidioides_immitis">coccidioides_immitis</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="culex">culex</option>
        <option value="debaryomyces_hansenii">debaryomyces_hansenii</option>
        <option value="E_coli_K12">E_coli_K12</option>
        <option value="elephant_shark">elephant_shark</option>
        <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option>
        <option value="eremothecium_gossypii">eremothecium_gossypii</option>
        <option value="fly">fly</option>
        <option value="fly_exp">fly_exp</option>
        <option value="fusarium">fusarium</option>
        <option value="fusarium_graminearum">fusarium_graminearum</option>
        <option value="galdieria">galdieria</option>
        <option value="generic">generic</option>
        <option value="heliconius_melpomene1">heliconius_melpomene1</option>
        <option value="histoplasma">histoplasma</option>
        <option value="histoplasma_capsulatum">histoplasma_capsulatum</option>
        <option value="honeybee1">honeybee1</option>
        <option value="human">human</option>
        <option value="japaneselamprey">japaneselamprey</option>
        <option value="kluyveromyces_lactis">kluyveromyces_lactis</option>
        <option value="laccaria_bicolor">laccaria_bicolor</option>
        <option value="leishmania_tarentolae">leishmania_tarentolae</option>
        <option value="lodderomyces_elongisporus">lodderomyces_elongisporus</option>
        <option value="magnaporthe_grisea">magnaporthe_grisea</option>
        <option value="maize">maize</option>
        <option value="maize5">maize5</option>
        <option value="mnemiopsis_leidyi">mnemiopsis_leidyi</option>
        <option value="nasonia">nasonia</option>
        <option value="nematostella_vectensis">nematostella_vectensis</option>
        <option value="neurospora">neurospora</option>
        <option value="neurospora_crassa">neurospora_crassa</option>
        <option value="parasteatoda">parasteatoda</option>
        <option value="pchrysosporium">pchrysosporium</option>
        <option value="pea_aphid">pea_aphid</option>
        <option value="pfalciparum">pfalciparum</option>
        <option value="phanerochaete_chrysosporium">phanerochaete_chrysosporium</option>
        <option value="pichia_stipitis">pichia_stipitis</option>
        <option value="pisaster">pisaster</option>
        <option value="pneumocystis">pneumocystis</option>
        <option value="rhincodon">rhincodon</option>
        <option value="rhizopus_oryzae">rhizopus_oryzae</option>
        <option value="rhodnius">rhodnius</option>
        <option value="rice">rice</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">s_aureus</option>
        <option value="schistosoma">schistosoma</option>
        <option value="schistosoma2">schistosoma2</option>
        <option value="schizosaccharomyces_pombe">schizosaccharomyces_pombe</option>
        <option value="scyliorhinus">scyliorhinus</option>
        <option value="sealamprey">sealamprey</option>
        <option value="s_pneumoniae">s_pneumoniae</option>
        <option value="strongylocentrotus_purpuratus">strongylocentrotus_purpuratus</option>
        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
        <option value="template_prokaryotic">template_prokaryotic</option>
        <option value="tetrahymena">tetrahymena</option>
        <option value="thermoanaerobacter_tengcongensis">thermoanaerobacter_tengcongensis</option>
        <option value="tomato">tomato</option>
        <option value="toxoplasma">toxoplasma</option>
        <option value="tribolium2012">tribolium2012</option>
        <option value="trichinella">trichinella</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="volvox">volvox</option>
        <option value="wheat">wheat</option>
        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
        <option value="yarrowia_lipolytica">yarrowia_lipolytica</option>
        <option value="zebrafish">zebrafish</option>
    </xml>

    <xml name="busco_species">
        <!-- list generated from a Funannotate database directory, with the "funannotate database -show-buscos command" -->
        <option value="eukaryota">eukaryota</option>
        <option value="metazoa">metazoa</option>
        <option value="nematoda">nematoda</option>
        <option value="arthropoda">arthropoda</option>
        <option value="insecta">insecta</option>
        <option value="endopterygota">endopterygota</option>
        <option value="hymenoptera">hymenoptera</option>
        <option value="diptera">diptera</option>
        <option value="vertebrata">vertebrata</option>
        <option value="actinopterygii">actinopterygii</option>
        <option value="tetrapoda">tetrapoda</option>
        <option value="aves">aves</option>
        <option value="mammalia">mammalia</option>
        <option value="euarchontoglires">euarchontoglires</option>
        <option value="laurasiatheria">laurasiatheria</option>
        <option value="fungi">fungi</option>
        <option value="dikarya">dikarya</option>
        <option value="ascomycota">ascomycota</option>
        <option value="pezizomycotina">pezizomycotina</option>
        <option value="eurotiomycetes">eurotiomycetes</option>
        <option value="sordariomycetes">sordariomycetes</option>
        <option value="saccharomycetes">saccharomycetes</option>
        <option value="saccharomycetales">saccharomycetales</option>
        <option value="basidiomycota">basidiomycota</option>
        <option value="microsporidia">microsporidia</option>
        <option value="embryophyta">embryophyta</option>
        <option value="protists">protists</option>
        <option value="alveolata_stramenophiles">alveolata_stramenophiles</option>
        <!-- These datasets are additional BUSCO orthodb 10 datasets, they are not yet bundled
             with funannonate db, but they can be used safely. -->
         <option value="acidobacteria_odb10">acidobacteria (orthodb 10)</option>
         <option value="aconoidasida_odb10">aconoidasida (orthodb 10)</option>
         <option value="actinobacteria_class_odb10">actinobacteria_class (orthodb 10)</option>
         <option value="actinobacteria_phylum_odb10">actinobacteria_phylum (orthodb 10)</option>
         <option value="actinopterygii_odb10">actinopterygii (orthodb 10)</option>
         <option value="agaricales_odb10">agaricales (orthodb 10)</option>
         <option value="agaricomycetes_odb10">agaricomycetes (orthodb 10)</option>
         <option value="alphabaculovirus_odb10">alphabaculovirus (orthodb 10)</option>
         <option value="alphaherpesvirinae_odb10">alphaherpesvirinae (orthodb 10)</option>
         <option value="alphaproteobacteria_odb10">alphaproteobacteria (orthodb 10)</option>
         <option value="alteromonadales_odb10">alteromonadales (orthodb 10)</option>
         <option value="alveolata_odb10">alveolata (orthodb 10)</option>
         <option value="apicomplexa_odb10">apicomplexa (orthodb 10)</option>
         <option value="aquificae_odb10">aquificae (orthodb 10)</option>
         <option value="arachnida_odb10">arachnida (orthodb 10)</option>
         <option value="archaea_odb10">archaea (orthodb 10)</option>
         <option value="arthropoda_odb10">arthropoda (orthodb 10)</option>
         <option value="ascomycota_odb10">ascomycota (orthodb 10)</option>
         <option value="aves_odb10">aves (orthodb 10)</option>
         <option value="aviadenovirus_odb10">aviadenovirus (orthodb 10)</option>
         <option value="bacillales_odb10">bacillales (orthodb 10)</option>
         <option value="bacilli_odb10">bacilli (orthodb 10)</option>
         <option value="bacteria_odb10">bacteria (orthodb 10)</option>
         <option value="bacteroidales_odb10">bacteroidales (orthodb 10)</option>
         <option value="bacteroidetes-chlorobi_group_odb10">bacteroidetes-chlorobi_group (orthodb 10)</option>
         <option value="bacteroidetes_odb10">bacteroidetes (orthodb 10)</option>
         <option value="bacteroidia_odb10">bacteroidia (orthodb 10)</option>
         <option value="baculoviridae_odb10">baculoviridae (orthodb 10)</option>
         <option value="basidiomycota_odb10">basidiomycota (orthodb 10)</option>
         <option value="bclasvirinae_odb10">bclasvirinae (orthodb 10)</option>
         <option value="betabaculovirus_odb10">betabaculovirus (orthodb 10)</option>
         <option value="betaherpesvirinae_odb10">betaherpesvirinae (orthodb 10)</option>
         <option value="betaproteobacteria_odb10">betaproteobacteria (orthodb 10)</option>
         <option value="boletales_odb10">boletales (orthodb 10)</option>
         <option value="brassicales_odb10">brassicales (orthodb 10)</option>
         <option value="burkholderiales_odb10">burkholderiales (orthodb 10)</option>
         <option value="campylobacterales_odb10">campylobacterales (orthodb 10)</option>
         <option value="capnodiales_odb10">capnodiales (orthodb 10)</option>
         <option value="carnivora_odb10">carnivora (orthodb 10)</option>
         <option value="cellvibrionales_odb10">cellvibrionales (orthodb 10)</option>
         <option value="cetartiodactyla_odb10">cetartiodactyla (orthodb 10)</option>
         <option value="chaetothyriales_odb10">chaetothyriales (orthodb 10)</option>
         <option value="cheoctovirus_odb10">cheoctovirus (orthodb 10)</option>
         <option value="chlamydiae_odb10">chlamydiae (orthodb 10)</option>
         <option value="chlorobi_odb10">chlorobi (orthodb 10)</option>
         <option value="chloroflexi_odb10">chloroflexi (orthodb 10)</option>
         <option value="chlorophyta_odb10">chlorophyta (orthodb 10)</option>
         <option value="chordopoxvirinae_odb10">chordopoxvirinae (orthodb 10)</option>
         <option value="chromatiales_odb10">chromatiales (orthodb 10)</option>
         <option value="chroococcales_odb10">chroococcales (orthodb 10)</option>
         <option value="clostridia_odb10">clostridia (orthodb 10)</option>
         <option value="clostridiales_odb10">clostridiales (orthodb 10)</option>
         <option value="coccidia_odb10">coccidia (orthodb 10)</option>
         <option value="coriobacteriales_odb10">coriobacteriales (orthodb 10)</option>
         <option value="coriobacteriia_odb10">coriobacteriia (orthodb 10)</option>
         <option value="corynebacteriales_odb10">corynebacteriales (orthodb 10)</option>
         <option value="cyanobacteria_odb10">cyanobacteria (orthodb 10)</option>
         <option value="cyprinodontiformes_odb10">cyprinodontiformes (orthodb 10)</option>
         <option value="cytophagales_odb10">cytophagales (orthodb 10)</option>
         <option value="cytophagia_odb10">cytophagia (orthodb 10)</option>
         <option value="delta-epsilon-subdivisions_odb10">delta-epsilon-subdivisions (orthodb 10)</option>
         <option value="deltaproteobacteria_odb10">deltaproteobacteria (orthodb 10)</option>
         <option value="desulfobacterales_odb10">desulfobacterales (orthodb 10)</option>
         <option value="desulfovibrionales_odb10">desulfovibrionales (orthodb 10)</option>
         <option value="desulfurococcales_odb10">desulfurococcales (orthodb 10)</option>
         <option value="desulfuromonadales_odb10">desulfuromonadales (orthodb 10)</option>
         <option value="diptera_odb10">diptera (orthodb 10)</option>
         <option value="dothideomycetes_odb10">dothideomycetes (orthodb 10)</option>
         <option value="embryophyta_odb10">embryophyta (orthodb 10)</option>
         <option value="endopterygota_odb10">endopterygota (orthodb 10)</option>
         <option value="enquatrovirus_odb10">enquatrovirus (orthodb 10)</option>
         <option value="enterobacterales_odb10">enterobacterales (orthodb 10)</option>
         <option value="entomoplasmatales_odb10">entomoplasmatales (orthodb 10)</option>
         <option value="epsilonproteobacteria_odb10">epsilonproteobacteria (orthodb 10)</option>
         <option value="euarchontoglires_odb10">euarchontoglires (orthodb 10)</option>
         <option value="eudicots_odb10">eudicots (orthodb 10)</option>
         <option value="euglenozoa_odb10">euglenozoa (orthodb 10)</option>
         <option value="eukaryota_odb10">eukaryota (orthodb 10)</option>
         <option value="eurotiales_odb10">eurotiales (orthodb 10)</option>
         <option value="eurotiomycetes_odb10">eurotiomycetes (orthodb 10)</option>
         <option value="euryarchaeota_odb10">euryarchaeota (orthodb 10)</option>
         <option value="eutheria_odb10">eutheria (orthodb 10)</option>
         <option value="fabales_odb10">fabales (orthodb 10)</option>
         <option value="firmicutes_odb10">firmicutes (orthodb 10)</option>
         <option value="flavobacteriales_odb10">flavobacteriales (orthodb 10)</option>
         <option value="flavobacteriia_odb10">flavobacteriia (orthodb 10)</option>
         <option value="fromanvirus_odb10">fromanvirus (orthodb 10)</option>
         <option value="fungi_odb10">fungi (orthodb 10)</option>
         <option value="fusobacteria_odb10">fusobacteria (orthodb 10)</option>
         <option value="fusobacteriales_odb10">fusobacteriales (orthodb 10)</option>
         <option value="gammaherpesvirinae_odb10">gammaherpesvirinae (orthodb 10)</option>
         <option value="gammaproteobacteria_odb10">gammaproteobacteria (orthodb 10)</option>
         <option value="glires_odb10">glires (orthodb 10)</option>
         <option value="glomerellales_odb10">glomerellales (orthodb 10)</option>
         <option value="guernseyvirinae_odb10">guernseyvirinae (orthodb 10)</option>
         <option value="halobacteria_odb10">halobacteria (orthodb 10)</option>
         <option value="halobacteriales_odb10">halobacteriales (orthodb 10)</option>
         <option value="haloferacales_odb10">haloferacales (orthodb 10)</option>
         <option value="helotiales_odb10">helotiales (orthodb 10)</option>
         <option value="hemiptera_odb10">hemiptera (orthodb 10)</option>
         <option value="herpesviridae_odb10">herpesviridae (orthodb 10)</option>
         <option value="hymenoptera_odb10">hymenoptera (orthodb 10)</option>
         <option value="hypocreales_odb10">hypocreales (orthodb 10)</option>
         <option value="insecta_odb10">insecta (orthodb 10)</option>
         <option value="iridoviridae_odb10">iridoviridae (orthodb 10)</option>
         <option value="lactobacillales_odb10">lactobacillales (orthodb 10)</option>
         <option value="laurasiatheria_odb10">laurasiatheria (orthodb 10)</option>
         <option value="legionellales_odb10">legionellales (orthodb 10)</option>
         <option value="leotiomycetes_odb10">leotiomycetes (orthodb 10)</option>
         <option value="lepidoptera_odb10">lepidoptera (orthodb 10)</option>
         <option value="liliopsida_odb10">liliopsida (orthodb 10)</option>
         <option value="mammalia_odb10">mammalia (orthodb 10)</option>
         <option value="metazoa_odb10">metazoa (orthodb 10)</option>
         <option value="methanobacteria_odb10">methanobacteria (orthodb 10)</option>
         <option value="methanococcales_odb10">methanococcales (orthodb 10)</option>
         <option value="methanomicrobia_odb10">methanomicrobia (orthodb 10)</option>
         <option value="methanomicrobiales_odb10">methanomicrobiales (orthodb 10)</option>
         <option value="micrococcales_odb10">micrococcales (orthodb 10)</option>
         <option value="microsporidia_odb10">microsporidia (orthodb 10)</option>
         <option value="mollicutes_odb10">mollicutes (orthodb 10)</option>
         <option value="mollusca_odb10">mollusca (orthodb 10)</option>
         <option value="mucorales_odb10">mucorales (orthodb 10)</option>
         <option value="mucoromycota_odb10">mucoromycota (orthodb 10)</option>
         <option value="mycoplasmatales_odb10">mycoplasmatales (orthodb 10)</option>
         <option value="natrialbales_odb10">natrialbales (orthodb 10)</option>
         <option value="neisseriales_odb10">neisseriales (orthodb 10)</option>
         <option value="nematoda_odb10">nematoda (orthodb 10)</option>
         <option value="nitrosomonadales_odb10">nitrosomonadales (orthodb 10)</option>
         <option value="nostocales_odb10">nostocales (orthodb 10)</option>
         <option value="oceanospirillales_odb10">oceanospirillales (orthodb 10)</option>
         <option value="onygenales_odb10">onygenales (orthodb 10)</option>
         <option value="oscillatoriales_odb10">oscillatoriales (orthodb 10)</option>
         <option value="pahexavirus_odb10">pahexavirus (orthodb 10)</option>
         <option value="passeriformes_odb10">passeriformes (orthodb 10)</option>
         <option value="pasteurellales_odb10">pasteurellales (orthodb 10)</option>
         <option value="peduovirus_odb10">peduovirus (orthodb 10)</option>
         <option value="planctomycetes_odb10">planctomycetes (orthodb 10)</option>
         <option value="plasmodium_odb10">plasmodium (orthodb 10)</option>
         <option value="pleosporales_odb10">pleosporales (orthodb 10)</option>
         <option value="poales_odb10">poales (orthodb 10)</option>
         <option value="polyporales_odb10">polyporales (orthodb 10)</option>
         <option value="poxviridae_odb10">poxviridae (orthodb 10)</option>
         <option value="primates_odb10">primates (orthodb 10)</option>
         <option value="propionibacteriales_odb10">propionibacteriales (orthodb 10)</option>
         <option value="proteobacteria_odb10">proteobacteria (orthodb 10)</option>
         <option value="pseudomonadales_odb10">pseudomonadales (orthodb 10)</option>
         <option value="rhizobiales_odb10">rhizobiales (orthodb 10)</option>
         <option value="rhizobium-agrobacterium_group_odb10">rhizobium-agrobacterium_group (orthodb 10)</option>
         <option value="rhodobacterales_odb10">rhodobacterales (orthodb 10)</option>
         <option value="rhodospirillales_odb10">rhodospirillales (orthodb 10)</option>
         <option value="rickettsiales_odb10">rickettsiales (orthodb 10)</option>
         <option value="rudiviridae_odb10">rudiviridae (orthodb 10)</option>
         <option value="saccharomycetes_odb10">saccharomycetes (orthodb 10)</option>
         <option value="sauropsida_odb10">sauropsida (orthodb 10)</option>
         <option value="selenomonadales_odb10">selenomonadales (orthodb 10)</option>
         <option value="simplexvirus_odb10">simplexvirus (orthodb 10)</option>
         <option value="skunavirus_odb10">skunavirus (orthodb 10)</option>
         <option value="solanales_odb10">solanales (orthodb 10)</option>
         <option value="sordariomycetes_odb10">sordariomycetes (orthodb 10)</option>
         <option value="sphingobacteriia_odb10">sphingobacteriia (orthodb 10)</option>
         <option value="sphingomonadales_odb10">sphingomonadales (orthodb 10)</option>
         <option value="spirochaetales_odb10">spirochaetales (orthodb 10)</option>
         <option value="spirochaetes_odb10">spirochaetes (orthodb 10)</option>
         <option value="spirochaetia_odb10">spirochaetia (orthodb 10)</option>
         <option value="spounavirinae_odb10">spounavirinae (orthodb 10)</option>
         <option value="stramenopiles_odb10">stramenopiles (orthodb 10)</option>
         <option value="streptomycetales_odb10">streptomycetales (orthodb 10)</option>
         <option value="streptosporangiales_odb10">streptosporangiales (orthodb 10)</option>
         <option value="sulfolobales_odb10">sulfolobales (orthodb 10)</option>
         <option value="synechococcales_odb10">synechococcales (orthodb 10)</option>
         <option value="synergistetes_odb10">synergistetes (orthodb 10)</option>
         <option value="tenericutes_odb10">tenericutes (orthodb 10)</option>
         <option value="tequatrovirus_odb10">tequatrovirus (orthodb 10)</option>
         <option value="teseptimavirus_odb10">teseptimavirus (orthodb 10)</option>
         <option value="tetrapoda_odb10">tetrapoda (orthodb 10)</option>
         <option value="tevenvirinae_odb10">tevenvirinae (orthodb 10)</option>
         <option value="thaumarchaeota_odb10">thaumarchaeota (orthodb 10)</option>
         <option value="thermoanaerobacterales_odb10">thermoanaerobacterales (orthodb 10)</option>
         <option value="thermoplasmata_odb10">thermoplasmata (orthodb 10)</option>
         <option value="thermoproteales_odb10">thermoproteales (orthodb 10)</option>
         <option value="thermoprotei_odb10">thermoprotei (orthodb 10)</option>
         <option value="thermotogae_odb10">thermotogae (orthodb 10)</option>
         <option value="thiotrichales_odb10">thiotrichales (orthodb 10)</option>
         <option value="tissierellales_odb10">tissierellales (orthodb 10)</option>
         <option value="tissierellia_odb10">tissierellia (orthodb 10)</option>
         <option value="tremellomycetes_odb10">tremellomycetes (orthodb 10)</option>
         <option value="tunavirinae_odb10">tunavirinae (orthodb 10)</option>
         <option value="varicellovirus_odb10">varicellovirus (orthodb 10)</option>
         <option value="verrucomicrobia_odb10">verrucomicrobia (orthodb 10)</option>
         <option value="vertebrata_odb10">vertebrata (orthodb 10)</option>
         <option value="vibrionales_odb10">vibrionales (orthodb 10)</option>
         <option value="viridiplantae_odb10">viridiplantae (orthodb 10)</option>
         <option value="xanthomonadales_odb10">xanthomonadales (orthodb 10)</option>
    </xml>
</macros>