Mercurial > repos > bgruening > augustus
changeset 11:534814b64234 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit b8194e4d746760fff7a7c5bb9c41df28089d9782
| author | iuc |
|---|---|
| date | Thu, 17 Jul 2025 09:06:01 +0000 |
| parents | 0fc0f9cf035a |
| children | |
| files | augustus.xml macros.xml test-data/augustus.hints.output.gtf test-data/augustus.hints_and_range.output.gtf test-data/human_augustus.fa.gz test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf test-data/human_augustus_utr-on_softmasking.gtf |
| diffstat | 9 files changed, 225 insertions(+), 207 deletions(-) [+] |
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--- 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>
--- a/macros.xml Sun Dec 15 09:09:57 2024 +0000 +++ b/macros.xml Thu Jul 17 09:06:01 2025 +0000 @@ -7,8 +7,8 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">3.4.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">3.5.0</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.1</token>
--- a/test-data/augustus.hints.output.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/augustus.hints.output.gtf Thu Jul 17 09:06:01 2025 +0000 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat ... +# reading in the file /tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat ... # Have extrinsic information about 1 sequences (in the specified range). # Initializing the parameters using config directory /usr/local/config/ ... # fly version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9950, name = chr2R) ----- @@ -44,7 +44,6 @@ # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 9303 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 9303 0.84 - . chr2R.g1.t1 -chr2R AUGUSTUS start_codon 9301 9303 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 57.1 # CDS exons: 4/4 @@ -59,4 +58,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/0/c/6/dataset_0c6b001d-370e-42cf-be92-b3435bd212c5.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/6/4/3/dataset_64360fd3-ce82-407d-a499-79ac51decbd9.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/8/6/b/dataset_86b0a149-1d37-4615-9915-2c48586e3ca1.dat --species=fly +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/7/b/a/dataset_7ba46cfd-42e9-4f8e-8875-e339c6728906.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/a/6/2/dataset_a62f021d-9ecd-4331-83ac-119ad4aac229.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/3/4/e/dataset_34e31244-f096-4c30-9f0d-5ca9e518e4bb.dat --species=fly
--- a/test-data/augustus.hints_and_range.output.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/augustus.hints_and_range.output.gtf Thu Jul 17 09:06:01 2025 +0000 @@ -1,17 +1,17 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # Sources of extrinsic information: M RM E W # Setting CDSpart local malus: 0.985 # Setting UTRpart local malus: 0.973 -# reading in the file /tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat ... +# reading in the file /tmp/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.dat ... # Have extrinsic information about 1 sequences (in the specified range). # Initializing the parameters using config directory /usr/local/config/ ... # fly version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.dat is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 2001, name = chr2R) ----- @@ -38,7 +38,6 @@ # start gene chr2R.g1 chr2R AUGUSTUS gene 7560 8931 0.84 - . chr2R.g1 chr2R AUGUSTUS transcript 7560 8931 0.84 - . chr2R.g1.t1 -chr2R AUGUSTUS start_codon 8929 8931 . - 0 transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1"; # Evidence for and against this transcript: # % of transcript supported by hints (any source): 60 # CDS exons: 3/3 @@ -53,4 +52,4 @@ # end gene chr2R.g1 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /tmp/tmpb49zmbej/files/4/c/8/dataset_4c80a809-791b-4afe-a497-698a7460ac31.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpb49zmbej/files/f/a/8/dataset_fa8684ad-0602-4c00-9999-b998db931a6e.dat --extrinsicCfgFile=/tmp/tmpb49zmbej/files/3/3/5/dataset_335e9fec-9340-42e6-97ce-af35d5220fcc.dat --predictionStart=7000 --predictionEnd=9000 --species=fly +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/6/d/9/dataset_6d9a0d6d-a406-4749-8cb1-1d06374faa38.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/tmp/tmpjsgft19_/files/2/8/2/dataset_2822734d-a594-477d-a8ef-82ffb21dcccf.dat --extrinsicCfgFile=/tmp/tmpjsgft19_/files/7/6/7/dataset_7673297f-b12d-48f2-b40c-2fcd8e18239d.dat --predictionStart=7000 --predictionEnd=9000 --species=fly
--- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Thu Jul 17 09:06:01 2025 +0000 @@ -1,13 +1,13 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/b/3/0/dataset_b30bd3b8-32ff-49ce-be3d-bdb824bd72df.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- @@ -98,4 +98,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/c/d/6/dataset_cd6650af-fd36-4176-b9f1-e38bb118655f.dat --UTR=off --genemodel=complete --softmasking=0 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/b/3/0/dataset_b30bd3b8-32ff-49ce-be3d-bdb824bd72df.dat --UTR=off --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on.gff Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_utr-on.gff Thu Jul 17 09:06:01 2025 +0000 @@ -1,14 +1,14 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- @@ -19,7 +19,6 @@ HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1 HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1 -HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1 @@ -77,7 +76,6 @@ HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1 HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1 -HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1 @@ -103,4 +101,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/e/0/1/dataset_e0109fd4-ac59-4275-90d3-25691349bc0c.dat --UTR=on --genemodel=complete --softmasking=0 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/2/a/c/dataset_2acd78b6-6b4d-4592-91d1-ec3a4dc4a8f0.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_utr-on.gtf Thu Jul 17 09:06:01 2025 +0000 @@ -1,13 +1,14 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat is in gzip format. Deflating... +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- @@ -18,7 +19,6 @@ HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; @@ -76,7 +76,6 @@ HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; -HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; @@ -102,4 +101,4 @@ # end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/6/0/5/dataset_605b6f62-4302-4e11-b378-848be921c4e4.dat --UTR=on --genemodel=complete --softmasking=0 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --start=off --stop=off --cds=on --singlestrand=false /tmp/tmpjsgft19_/files/a/4/8/dataset_a48be2bb-95b9-461d-aa42-cc5ff0ce9360.dat --UTR=on --genemodel=complete --softmasking=0 --species=human
--- a/test-data/human_augustus_utr-on_softmasking.gtf Sun Dec 15 09:09:57 2024 +0000 +++ b/test-data/human_augustus_utr-on_softmasking.gtf Thu Jul 17 09:06:01 2025 +0000 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.4.0). +# This output was generated with AUGUSTUS (version 3.5.0). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), -# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. +# O. Keller, S. König, L. Gerischer, L. Romoth, Katharina Hoff, Henry Mehlan and Daniel Honsel. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 @@ -8,7 +8,7 @@ # Sources of extrinsic information: M RM # Initializing the parameters using config directory /usr/local/config/ ... # human version. Using default transition matrix. -# Looks like /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat is in fasta format. +# Looks like /tmp/tmpjsgft19_/files/0/e/e/dataset_0ee7b75a-3ef6-4edb-811b-e06e2e5fae27.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- @@ -21,4 +21,4 @@ # Predicted genes for sequence number 2 on both strands # (none) # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpb49zmbej/files/1/1/4/dataset_11447207-979d-4b84-a63d-14dd1e776f0e.dat --UTR=on --genemodel=complete --softmasking=1 --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --start=off --stop=off --cds=off --singlestrand=false /tmp/tmpjsgft19_/files/0/e/e/dataset_0ee7b75a-3ef6-4edb-811b-e06e2e5fae27.dat --UTR=on --genemodel=complete --softmasking=1 --species=human