<tool id="augustus" name="Augustus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>gene prediction for prokaryotic and eukaryotic genomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">augustus</xref>
    </xrefs>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
        #if $model.augustus_mode == 'history'

            ## Using an augustus model from history, we need to unzip it and let augustus find it

            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 &&

            export AUGUSTUS_CONFIG_PATH=./augustus_dir/ &&
        #end if

        ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external
        ## script is used to extract the sequences into additional files

        augustus
            --strand=$strand
            $noInFrameStop
            $gff
            --uniqueGeneId=true

            #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'
            $utr
            --genemodel=$genemodel
            --softmasking=$softmasking
            #if $hints.usehints == 'T'
                --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
            #end if

            #if $range.userange == 'T'
                --predictionStart=$range.start --predictionEnd=$range.stop
            #end if

            #if $model.augustus_mode == 'history'
                --species=local
            #else
                --species=$model.organism
            #end if

        | tee '$output'
        #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','):
            | python $__tool_directory__/extract_features.py
                #if 'protein' in str($outputs).split(','):
                    --protein $protein_output
                #end if
                #if 'codingseq' in str($outputs).split(','):
                    --codingseq $codingseq_output
                #end if
        #end if
]]>
    </command>
    <inputs>
        <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"
            help="Otherwise, intron-spanning stop codons could occur." />
        <param type="boolean" argument="--singlestrand"
            label="Predict genes independently on each strand"
            help="This allows overlapping genes on opposite strands."
            truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />

        <param name="utr" type="boolean" argument="--UTR"
            label="Predict the untranslated regions in addition to the coding sequence"
            truevalue="--UTR=on" falsevalue="--UTR=off" checked="false"
            help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />


        <conditional name="model">
            <param name="augustus_mode" type="select" label="Trainingset">
                <option value="builtin">Run Augustus with a predefined trainingset</option>
                <option value="history">Run Augustus with a custom trainingset</option>
            </param>
            <when value="history">
                <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. 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) -->
                    <!-- 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="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="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="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="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="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="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="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="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">
            <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>
            <option value="partial">partial</option>
            <option value="intronless">intronless</option>
            <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>
                <option value="T">Yes</option>
            </param>
            <when value="T">
                <param argument="--hintsfile" label="Select hints file from history" type="data" format="gff"
                    help="A file containing hints in gff format"/>
                <param name="extrinsiccfg" argument="--extrinsicCfgFile" label="Select extrinsic configuration file from history" type="data" format="txt"
                    help="A .cfg file listing hint sources and their boni and mali"/>
            </when>
            <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>
                <option value="T">Yes</option>
            </param>
            <when value="T">
                <param name="start" argument="--predictionStart" label="Starting position" type="integer" value=""
                    help="The beginning of the search range"/>
                <param name="stop" argument="--predictionEnd" label="Ending position" type="integer" value=""
                    help="The end of the search range; must be greater than starting position"/>
            </when>
            <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" 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>
            <option value="cds" selected="true">CDS region (--cds)</option>
        </param>
    </inputs>
    <outputs>
        <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF">
            <change_format>
                <when input="gff" value="--gff3=on" format="gff3" />
            </change_format>
        </data>
        <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence">
            <filter>outputs and 'protein' in outputs</filter>
        </data>
        <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence">
            <filter>outputs and 'codingseq' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <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" />
            <conditional name="model">
                <param name="organism" value="human" />
            </conditional>
            <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 expect_num_outputs="3">
            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
            <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"/>
            <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" />
        </test>
        <test expect_num_outputs="1">
            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
            <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">
                <assert_contents>
                    <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
                </assert_contents>
            </output>

        </test>
        <test expect_num_outputs="1">
            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
            <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_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" />
                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
                </assert_contents>
            </output>
        </test>
        <!-- Test softmasking parameter-->
        <test expect_num_outputs="1">
            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
            <conditional name="model">
                <param name="organism" value="human" />
            </conditional>
            <param name="utr" value="True" />
            <param name="softmasking" value="True"/>
            <param name="outputs" value_json="null"/>
            <output name="output" file="human_augustus_utr-on_softmasking.gtf" ftype="gtf" lines_diff="6"/>
        </test>

    </tests>
    <help>
<![CDATA[

**What it does**

AUGUSTUS is a gene prediction program for prokaryotes and eukaryotes written by Mario Stanke and Oliver Keller.
It can be used as an ab initio program, which means it bases its prediction purely on the
sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
such as EST, MS/MS, protein alignments and synthenic genomic alignments.


**Input**

Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence.


**Output**

Augustus produces three output files: a FASTA file with predicted coding sequences, a FASTA file with predicted protein sequences and a gtf/GFF output file if selected.


**Parameters**

Gene Model:

partial:    allow prediction of incomplete genes at the sequence boundaries (default)
intronless: only predict single-exon genes like in prokaryotes and some eukaryotes
complete:   only predict complete genes
atleastone: predict at least one complete gene
exactlyone: predict exactly one complete gene



**Example**

Suppose you have the following DNA FASTA sequence:

>Seq1
cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg


Running this tool will produce this:

    # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----
    #
    # Constraints/Hints:
    # (none)
    # Predicted genes for sequence number 1 on both strands
    # start gene g1
    scaffold1|size1992969	AUGUSTUS	gene	17453	19382	0.11	+	.	g6
    scaffold1|size1992969	AUGUSTUS	transcript	17453	19382	0.11	+	.	g6.t1
    scaffold1|size1992969	AUGUSTUS	start_codon	17453	17455	.	+	0	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	intron	17615	17660	0.38	+	.	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	intron	17708	17772	0.54	+	.	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	intron	17902	18035	0.58	+	.	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	intron	18313	18367	0.99	+	.	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	intron	19014	19080	0.44	+	.	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	17453	17614	0.55	+	0	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	17661	17707	0.38	+	0	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	17773	17901	0.54	+	1	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	18036	18312	0.52	+	1	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	18368	19013	0.99	+	0	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	CDS	19081	19379	0.31	+	2	transcript_id "g6.t1"; gene_id "g6";
    scaffold1|size1992969	AUGUSTUS	stop_codon	19380	19382	.	+	0	transcript_id "g6.t1"; gene_id "g6";


]]>
    </help>
    <expand macro="citations"/>
</tool>