| Previous changeset 11:8e1ace8f77c6 (2024-06-26) Next changeset 13:19ddd5557b4f (2025-03-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4 |
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modified:
funannotate_clean.xml macros.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/funannotate_db/outgroups/botrytis_cinerea.dikarya_buscos.fa test-data/funannotate_options.loc |
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| diff -r 8e1ace8f77c6 -r 5c09ad60911c funannotate_clean.xml --- a/funannotate_clean.xml Wed Jun 26 09:41:06 2024 +0000 +++ b/funannotate_clean.xml Fri Mar 07 22:34:18 2025 +0000 |
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| @@ -21,9 +21,9 @@ <inputs> <param argument="--input" type="data" format="fasta" label="Assembly to clean" /> - <param argument="--pident" type="integer" value="95" label="Percent identity of overlap" /> - <param argument="--cov" type="integer" value="95" label="Percent coverage of overlap" /> - <param argument="--minlen" type="integer" value="500" label="Minimum length of contig to keep" /> + <param argument="--pident" type="integer" value="95" min="0" max="100" label="Percent identity of overlap" /> + <param argument="--cov" type="integer" value="95" min="0" max="100" label="Percent coverage of overlap" /> + <param argument="--minlen" type="integer" min="0" value="500" label="Minimum length of contig to keep" /> <param argument="--exhaustive" type="boolean" checked="false" truevalue="--exhaustive" falsevalue="" label="Test every contig" help="Default is to stop at N50 value" /> </inputs> |
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| diff -r 8e1ace8f77c6 -r 5c09ad60911c macros.xml --- a/macros.xml Wed Jun 26 09:41:06 2024 +0000 +++ b/macros.xml Fri Mar 07 22:34:18 2025 +0000 |
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| b'@@ -1,7 +1,7 @@\n <?xml version="1.0"?>\n <macros>\n- <token name="@TOOL_VERSION@">1.8.15</token>\n- <token name="@VERSION_SUFFIX@">5</token>\n+ <token name="@TOOL_VERSION@">1.8.17</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n <xml name="biotools">\n <xrefs>\n <xref type="bio.tools">\n@@ -19,342 +19,24 @@\n </citations>\n </xml>\n \n- <xml name="augustus_species">\n- <!-- list generated from a Funannotate database directory, listing trained_species/* -->\n- <option value="adorsata">adorsata</option>\n- <option value="aedes">aedes</option>\n- <option value="amphimedon">amphimedon</option>\n- <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>\n- <option value="anidulans">anidulans</option>\n- <option value="arabidopsis">arabidopsis</option>\n- <option value="aspergillus_fumigatus">aspergillus_fumigatus</option>\n- <option value="aspergillus_nidulans">aspergillus_nidulans</option>\n- <option value="aspergillus_oryzae">aspergillus_oryzae</option>\n- <option value="aspergillus_terreus">aspergillus_terreus</option>\n- <option value="bombus_impatiens1">bombus_impatiens1</option>\n- <option value="bombus_terrestris2">bombus_terrestris2</option>\n- <option value="botrytis_cinerea">botrytis_cinerea</option>\n- <option value="b_pseudomallei">b_pseudomallei</option>\n- <option value="brugia">brugia</option>\n- <option value="cacao">cacao</option>\n- <option value="caenorhabditis">caenorhabditis</option>\n- <option value="camponotus_floridanus">camponotus_floridanus</option>\n- <option value="candida_albicans">candida_albicans</option>\n- <option value="candida_guilliermondii">candida_guilliermondii</option>\n- <option value="candida_tropicalis">candida_tropicalis</option>\n- <option value="c_elegans_trsk">c_elegans_trsk</option>\n- <option value="chaetomium_globosum">chaetomium_globosum</option>\n- <option value="chicken">chicken</option>\n- <option value="chiloscyllium">chiloscyllium</option>\n- <option value="chlamy2011">chlamy2011</option>\n- <option value="chlamydomonas">chlamydomonas</option>\n- <option value="chlorella">chlorella</option>\n- <option value="ciona">ciona</option>\n- <option value="coccidioides_immitis">coccidioides_immitis</option>\n- <option value="Conidiobolus_coronatus">Conidiobolus_coronatus</option>\n- <option value="coprinus">coprinus</option>\n- <option value="coprinus_cinereus">coprinus_cinereus</option>\n- <option value="coyote_tobacco">coyote_tobacco</option>\n- <option value="cryptococcus">cryptococcus</option>\n- <option value="cryptococcus_neoformans_gattii">cryptococcus_neoformans_gattii</option>\n- <option value="cryptococcus_neoformans_neoformans_B">cryptococcus_neoformans_neoformans_B</option>\n- <option value="cryptococcus_neoformans_neoformans_JEC21">cryptococcus_neoformans_neoformans_JEC21</option>\n- <option value="culex">culex</option>\n- <option value="debaryomyces_hansenii">debaryomyces_hansenii</option>\n- <option value="E_coli_K12">E_coli_K12</option>\n- <option value="elephant_shark">elephant_shark</option>\n- <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option>\n- <option value="eremothecium_gossypii">eremothecium_gossypii</option>\n- <option value="fly">fly</option>\n- <option value="fly_exp">fly_exp</option>\n- <option value="fusarium">fusarium</option>\n- <option value="fusarium_graminearum">fusarium_graminearum</option>\n- <option value="galdieria">galdieria</option>\n- <option value="generic">generic</option>\n- <option value="heliconius_melpomene1">heliconius_melpomene1</option>\n- <option value="histoplasma">histoplasma</option>\n- <option value="histoplasma_capsulatum">his'..b'irillales_odb10">rhodospirillales (orthodb 10)</option>\n- <option value="rickettsiales_odb10">rickettsiales (orthodb 10)</option>\n- <option value="rudiviridae_odb10">rudiviridae (orthodb 10)</option>\n- <option value="saccharomycetes_odb10">saccharomycetes (orthodb 10)</option>\n- <option value="sauropsida_odb10">sauropsida (orthodb 10)</option>\n- <option value="selenomonadales_odb10">selenomonadales (orthodb 10)</option>\n- <option value="simplexvirus_odb10">simplexvirus (orthodb 10)</option>\n- <option value="skunavirus_odb10">skunavirus (orthodb 10)</option>\n- <option value="solanales_odb10">solanales (orthodb 10)</option>\n- <option value="sordariomycetes_odb10">sordariomycetes (orthodb 10)</option>\n- <option value="sphingobacteriia_odb10">sphingobacteriia (orthodb 10)</option>\n- <option value="sphingomonadales_odb10">sphingomonadales (orthodb 10)</option>\n- <option value="spirochaetales_odb10">spirochaetales (orthodb 10)</option>\n- <option value="spirochaetes_odb10">spirochaetes (orthodb 10)</option>\n- <option value="spirochaetia_odb10">spirochaetia (orthodb 10)</option>\n- <option value="spounavirinae_odb10">spounavirinae (orthodb 10)</option>\n- <option value="stramenopiles_odb10">stramenopiles (orthodb 10)</option>\n- <option value="streptomycetales_odb10">streptomycetales (orthodb 10)</option>\n- <option value="streptosporangiales_odb10">streptosporangiales (orthodb 10)</option>\n- <option value="sulfolobales_odb10">sulfolobales (orthodb 10)</option>\n- <option value="synechococcales_odb10">synechococcales (orthodb 10)</option>\n- <option value="synergistetes_odb10">synergistetes (orthodb 10)</option>\n- <option value="tenericutes_odb10">tenericutes (orthodb 10)</option>\n- <option value="tequatrovirus_odb10">tequatrovirus (orthodb 10)</option>\n- <option value="teseptimavirus_odb10">teseptimavirus (orthodb 10)</option>\n- <option value="tetrapoda_odb10">tetrapoda (orthodb 10)</option>\n- <option value="tevenvirinae_odb10">tevenvirinae (orthodb 10)</option>\n- <option value="thaumarchaeota_odb10">thaumarchaeota (orthodb 10)</option>\n- <option value="thermoanaerobacterales_odb10">thermoanaerobacterales (orthodb 10)</option>\n- <option value="thermoplasmata_odb10">thermoplasmata (orthodb 10)</option>\n- <option value="thermoproteales_odb10">thermoproteales (orthodb 10)</option>\n- <option value="thermoprotei_odb10">thermoprotei (orthodb 10)</option>\n- <option value="thermotogae_odb10">thermotogae (orthodb 10)</option>\n- <option value="thiotrichales_odb10">thiotrichales (orthodb 10)</option>\n- <option value="tissierellales_odb10">tissierellales (orthodb 10)</option>\n- <option value="tissierellia_odb10">tissierellia (orthodb 10)</option>\n- <option value="tremellomycetes_odb10">tremellomycetes (orthodb 10)</option>\n- <option value="tunavirinae_odb10">tunavirinae (orthodb 10)</option>\n- <option value="varicellovirus_odb10">varicellovirus (orthodb 10)</option>\n- <option value="verrucomicrobia_odb10">verrucomicrobia (orthodb 10)</option>\n- <option value="vertebrata_odb10">vertebrata (orthodb 10)</option>\n- <option value="vibrionales_odb10">vibrionales (orthodb 10)</option>\n- <option value="viridiplantae_odb10">viridiplantae (orthodb 10)</option>\n- <option value="xanthomonadales_odb10">xanthomonadales (orthodb 10)</option>\n+\n+ <xml name="busco_seeds">\n+ <options from_data_table="funannotate_options">\n+ <column name="value" index="0" />\n+ <column name="name" index="1" />\n+ <filter type="static_value" column="2" value="trained_species"/>\n+ <filter type="param_value" column="3" ref="database"/>\n+ <yield/>\n+ </options>\n </xml>\n </macros>\n' |
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| diff -r 8e1ace8f77c6 -r 5c09ad60911c test-data/funannotate_db/outgroups/botrytis_cinerea.dikarya_buscos.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/outgroups/botrytis_cinerea.dikarya_buscos.fa Fri Mar 07 22:34:18 2025 +0000 |
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| b'@@ -0,0 +1,2042 @@\n+>EOG09260KCW\n+MLIVHDLKADTQRWLSQTNGPPGHYNFPPGTIIMKFGEQLRSSVIKEYQWYYIAYDELKEKLKTPYVTPSKKNKSSSKRQEWTEANEREFIDLMEAELDKVHTKQKLKAIEISRRIANADREVSEVVGRLDSRGPERSNGSVDSDAPTEEEFMLLEEDLSDIIADVHDLAKFVQLNYTGFQKIIKKHDKTTKWMLKPVFATRLKAKPFFKDNYDADIVKLSKLYDLVRTRGNPVQGDSSAGGSQASFIRQTTKYWVHPDNITELKLIILKHLPVLVFNASKEFEAKDSAITSIYYDNPETWDLYEGRLKKSEGAEAIRLRWYGDVDNEHIFVERKTHREDWTGEKSVKARFGIKEKNVNAYMKGEMLPAAIFEKARKEGKKPLKAIEEDERLAREVQYSVIKKGYVPVCRSFYNRTAFQLPADARVRISLDTELTMVREDNLDGKRRAGNNWRRMDIGIDYPFSQLPAEDVERFPYAVLEVKLQTQAGQEPPEWVRELIASHLVEAVPKFSKFIHGTATLFPTRINLIPFWMPQMDVDIRKPVTQSFGIKRPGHSNPSSTSDDDDDDDSDDEDYAFNQSGAGAIAAASETLRRRNHGATGNSLDIEEEISSMPLLEEDYIYDTDDEESIDNRPFERARRVGGLAFITEGIKYYAKTAGHHLSRKIHSISPTPRDPMDSNNATFSALRNGGGKIVAKKFKAPPGKKIHVPVRVEPKVYFAAERTFLTWLEFSIYIGTIAATLVNFGTKPTAVSFIVSGFFSIVAIMSLAYSVGMYLYRSNSIRERRNIKYYDAWGPSILCASLFAAVVVNAWFEMSAKE\n+>EOG09264SUZ\n+MASIARSLRPCASKITSSPFKTVPSWRSSSFGAVRAFSVSRAAFNKKYTKDHEWILLSPDNKTGTIGISDYAAHALGDVVYVELPTVPLDVGAGDAIGAVESVKSASDINSPIACKIVQANKMLEETPSTINKGPEDETSAGGWVAKVEVGEQGVKDLEGLMDESAYKAFIEE\n+>EOG092612XD\n+MVSNNKKRKRDTNKEDQDRQVNKAPKSGGSEKEVLLQEILALGGTEEDLDLVLDAQSDSENEAKPTTKSKDKDFKNEFAKFVAGLGIEGQAPEAEADEEDEEGDADDWRDEALQSESESSEPEEAPKVPEKSATKVKESSKTSKAAEKPAAVQVKESVKDQNRLNFEARPDWHAADLPILPAGDFSETGPYRSSINNLNEYAKALLEADSTLYASKHLSATSSHRFLATIMSSGTLSDKISALTLVVQESPVHTTRSFESLLDLAKKRSRGQAVTALGAMKDLLGAGVVLPADRRLRTFASQPGLLGTLQESDTGVWKSGQPLPGNMTKAHLISWAYEDWLKESYFDMLKILEVWCSDEVEYARSRAVMYVYELLKDKPEQESNLLRLLVNKLGDPDKKIASRSSYLLMQLQTSHPLMKPIIINSIENELILRPGQSSHAKYYAINTLNQTILSSKEEEVAKKLLSIYFGLFVSLLKKPEVIKPTGPKLNKKGEIQGGGGAMGKKAKEKLTAEEEAKQASEETTEKMISAVLTGVNRAFPFTKTDDLTLEKHMDTLFRITHSSNFNTSIQALMLIEQLSTTKHLAVDRFYRTLYESLLDPRLITSSKHALYLNLLYRALKSDVNIKRVKAFTKRMLQVVTLHQPPFICGIIYLLRELEVTFPGLKTLLNTPEANDEEEEEVYRDVPEEGETADIQATIAPSKPRTDTYDGKKRDPEHSNADKSCLWEIIPFLRHFHPSVSLFVDRLINDEKMPPKPDLASHTLTHFLDRFVYRNAKAAAGAPKGSSLMQPLAGGASQGILVSNRGTKVQQSVNSEAFWRKKAEDVAVDEVFFHKYFNQIGKGKDASKKKEKKKGEDGEDDEDEDEDEIWQALVESKPDIEGPESDDDDLNMDDFDMSEDDSEGGVDIEGSDEEVDVEGEDEDEDMQDAEEDDGEGIFSEEDDDLKDSDDEAGSDMDALFEAELQRAKSPEAEEEKKETSRSKKRKLKNLPTFASAEDYAAMLDKDDGDEDMGMGNGKGR\n+>EOG09260VTN\n+MSAEPDHVEHKKKVNLNDASGAEHKGNDDIATAILKKKKKPNSLMVTDAINDDNSVIALSNNTMETLQLFRGDTVLVKGKKRKDTVLIVLADDDLDDGSARMNRVVRHNLRVKHGDVITVHPCPDIKYAKRIAVLPIADTVEGLTGSLFDVFLAPYFREAYRPVRQGDLFTVRGGMRQVEFKVVEVDPPEYGIVAQDTVIHCEGEPIQREDEEGNLNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKSIGIKPPRGVLMFGPPGTGKTLMARAVANETGAFFFLINGPEIMSKMAGESESNLRKAFEEAEKNSPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVMAATNRPNSIDPALRRFGRFDREVDIGIPDPTGRLEILQIHTKNMKLGEDVDLEQIASETHGYVGSDVASLCSEAAMQQIREKMDLIDLDEDTIDAEVLDSLGVTMDNFRFALGVSNPSALREVAVVEVPNVRWDDIGGLEEVKRELIESVQYPVDHPEKFLKFGLSPSRGVLFYGPPGTGKTLLAKAVANECSANFISVKGPELLSMWFGESESNIRDIFDKARAAAPCVVFLDELDSIAKSRGGSNGDAGGASDRVVNQLLTEMDGMTSKKNVFVIGATNRPEQLDNALCRPGRLDTLVYVPLPNESSRAGILKAQLRKTPVADDVDLSYIASRTHGFSGADLGFITQRAVKLAIKESISLDIERRKALEAAGGDVDMEEEDVEDPVPKLTKAHFEEAMSQARRSVSDVEIRRYEAFAQSMKSSGPGAFFKFPEAGEAAEANGGGAAGFGDAGNDDSLYD\n+>EOG09261DG0\n+MSEVGAPIRNRLLRSKQDEASRINSSRKRKLRELFAVCDNEGPIPVILGIDSNAPPTNSAEAQFLEACDILQDRPFNESNLPARRQLRSDSLKQKSAIRQTGKDLLVKDASHKIEHYFKSDGAIPRKSRGTPPIENSNEGRNIERNGDDVRATAAATGVSIRRSPSKSLQTNSPTESSADIISSVEEAPEIASHLTNAAQSQQQQHDLSSRNFEVDRIKTVVESPPGSPGVNPREAVPPSAEDVANLQEPVIFGANDENHHAATAHLPPKEVQEARIEEMEKAREHTGDRGRHSITNSLRIAVDLPSSPSSTIDAHSTTTPARHDVSADTSPENDNSRYEEAKNPDNDVDLKPSTEPKSNREDIAQEDEHNSRHKTQNELSSTEALGSNSMSADAQLRMEDQAAAGSKIAAVTEIADSEASSSQGAEDLKLLAQQDRNSEKKIAVERAGDGANASLADETVRSEKVRPTPKANEVPDSEGEGQTPVDAMDLDVASVKDSSESQTTLESGPITNAKEPTSVLEETPMQMPSDAKTPPSAMSTPTTRKASSSTPVPVQAPIERMTTRVASGAIRHKSVSEILGETPAPNTSPTSARSPVSKLDTESAVNSPSRGSTPGSTRSLLQKSKEKNQSRLSTVVFAKKPTPGPRVNDITLVPRGANSHAAHAASPYDDYFACLYLNSHNTQKTGYPPLDGLLQTAHKTITTSNAFVPITENQTTRILKRIYGLQNTSKWSLRQPKRSEEPIRPTTHWDVLLQEAKWMRTDFREERKWKMAVAKNLAYACAEWFEASVEERKILQVNATRPALVLAETSKDVEMDDETSKSLSHPTPELIASAEFDSPMDDVDDELRLSLIDTVSPTAIFGLQDDDVVFGLSRSPATDKLLEELPLYGAPLSVPCNDLPTSEVDPDRFWRRPAVGISKYVEGRMELKFQGPSRKRSRFEYEEDSEDEDAEIDESRREKSLLPPEQTNIGLFDPANKHIRDRIHAGHQFRPPSEFPMPVQSFFENRSCSQWTCSEDDELKRHVREYAYNWSLISNMLSSRSLFSSGAERRTPWECFERWIALEGLPA'..b'KRLHGVSFKKRAPKAIKEIKAFATLSMGTTDVRLDPQLNKKVWEAGIKGVPFRLRVRISRKRNDEEGAKEKLYSYVQAVNVQNPKGLHTVVVEDA\n+>EOG09260Z5E\n+MVAVATNGNGPQDAFTPVIAALNTMRDGQRGQKEAAHSFLESFQKSAEAWQITIGILSSNAEPDAKLFAATTLRGKITYDVQQIPSDSLPALRNQLLELLKVFATGPRPIRIQLCVCLAILAIQMTTWKDVVPMVVSTLGNSAESLACVLDFLKVLPEEVTEGRKITLTEDELQQRTQELLGDNTAQVVQLLIAYAQSSESAATNPQLLEVITSWLREVPVADIVNSPLLPVIFNALNNDRSFEAATDCLCAIFKETREVDEYMPTIEILLPRVLALQPRIAQAAQEEDSESFKGFTRIFAEAGEAWVVLIAREPKVFRPLVEAILECTHRDFDKDAISLTFIFWYELKLYLILEMYIEARMQYVDVYSSLVDIMMKHLEFPTADGADETDLFDGDRDAEEKFREFRHHMGDVLKDCCEIMGVTPCLTKVYDAIKAWMGSYASQATAASVPHWQQLEAPLFESQFQYIVSSFTTDSKEIVRAAAMAMKFICSDCKHLLGGQVVQLQQFYDQTLDKLPGVSQEELTEGVASVVAVQPPSQTYQLMKLYCDPLMSRLMALANQANDEESKLQVADHMQLITLFIQIVTPWIESSQDHPAVKYCQEIFPILSTILDSFMTFTPICERVCRTWRYMIISYRTSMAPLLPQMANKLAEGFAASRQGCFLWVTSAILREFSEDREHVDEQTTESIYTFFEAQSTAMLKAMADLPPQDLPDVIEDFYRLLLDALLYYPHKMIRSHLFTPIFRAAIAALDLEQREPLSAVLHYIRDVISYGGDNPSSSASNINPPEIQQLVRQLILANGNDGVLLGLFEILPQETASWVDGILRMLPAGTVREAEIDRLMNSIREKLSIGHDGVRKVRSLLQDFTNTYRRRYVAPRDGLGRLEATRFQYSG\n+>EOG092644TW\n+MPRQFFVGGNFKMNGSVDSIKKIVGNLNDAKLDPNTEVVIAPPALYLLLTREHLRPGLEVAAQNVFDKPNGAFTGEISVEQLKDSNITWTLLGHSERRVILQEDDSFVACKTKAALDGGVGVIFCCGETLEQRESNKTIEVVTAQLKAVKDKVQDWSKIVIAYEPIWAIGTGKVASTEQAQEVHAAIRSWLKKEVSEKAAEETRIIYGGSVSEKNCKDLSKQEDIDGFLVGGASLKPAFVDIINSHL\n+>EOG09261NLR\n+MEAVLKGRAMCPFLQKTSPATLRSLSTSTRPHASPGGGSMSNLQTIAGRCPVMGKALAVQTAKAGKVGFGGVTAMKAIRAFSGKVSSGKAKLHTSRSHEARAVEDNIFGRENVPFPHIKQTRPPTQATRHEQSKAPKFDYEGFYNAELEKKHKDKSYRYFNNINRLAKEFPRAHMADKNEKVTVWCSNDYLGMGRNPQVLKAMHETLDVYGAGAGGTRNISGHNQHAVGLEASIAKLHAKDAALVFTSCYVANDATLATLGSKLPDCVFLSDSLNHASMIQGIRHSGAKKMVFKHNDLEDLEAKLASLPREVPKIIAFESVYSMCGSIGPIEGICDLAEKYGALTFLDEVHAVGMYGPHGAGVAEHLDYEAHLAGRPRGTIMDRVDIITGTLGKAYGCVGGYIAGSHKMVDAIRSLAAGFIFTTSLPPATMAGAQAAIEYQSEYQGDRRLQQLHTRAVKDSLSERDIPVIPNPSHIIPVLVGNAELAKRASDMLLDVHGIYVQSINYPTVPVGQERLRITPTPGHVREYREHLVNAIDSVFTELGIKRTSEWAAEGGFIGVGEAGGEVPEPLWTDEQLGVDQIVKEMKAAGPVGVMEALLERETKETAKAVSAAAQ\n+>EOG09265HP0\n+MIQLKTMLNCIDNSGAAVVECAKVLKMKRHAKIGDRIIVVVQKQRNFSESGPGASVSTSAANKVRRGDIRHAVVVRTVKKLQRPDGSVVKFDDNACVLINKAGEPIGTRLNGVVGTELRKMKWSKILSLAPMHL\n+>EOG09262SI7\n+MTITCAGTLQTMNVLMCQESLWLDLDILLSALAARLALPSTELLEIVFVDFELYAVILSTPEVHIFEDPTPSIRKDDLPKLSDEELYDVYEISRTVNEIREGGWKKIALQFSDGMLSDAPRVFQELESRLRKLPAEPSSSGIPKDEGSSLETDFSSPPANVATSNVRHKLYILADTSYGSCCVDEIAAEHVDAQVVIHYGRACLSPTARLPVIYVFTSRPLNLESVIQAFENTYKEKSEKIVIMADITYHSHISSLVAQLRDRGFENILAPEITHNPSATIPNRKLDEGVDMKDYSLFHISEPPSALLLTLSSRVKEMHIYSTDSTTGNETTKTNTARALMRRYALLTSQSSSSVFGILINTLSVTNYLPTVNSLASLIRSKGKKSYTFVVGKVNAAKLANFSEIDGWVVVGCWESSLVEGEALFKPVITPFELALALQSDDERVWGGDWVADFNALNLQANAVPTSSADPTETKTQDSEAVNPTEDAEDSEEESMPPEFDFRTGRYVSHSRPMRSSQTTSSEPKKALENGLQPNASNKLVKRAKMEMATVNGEVSPGAEYLREKRTWTGLGSDYDKEAIDEGREREVAAVVEEGRSGVARGYTVGEDASRS\n+>EOG09265K5D\n+MSRAAKLTLFGTSLFAASTIVFVHYAQTAEKAAMHAGVIRDMEQQRIKKERQLDFDLQRAMEEEYRKVQNVSDGTTR\n+>EOG092652ZZ\n+MSGPQDAQLFDEHFTVNELDHKKYVRVGRIKATSTVDHSVSMLLDINTELFPLAVGDNIRVVLATSLNLDGTKDDGKGWRDANRMGLGGEASLADMFDYVCHGKIYKFEDQENSDLIKAYISFGGLLMGLEGPYKKLTPLRVDYVYLLVKK\n+>EOG09261YLQ\n+MSHTNNDWAADDEEEEEDEYGYEDDDGDDFGLPSISSKKRKNQSRLKSASANTTVDEGKTPPWRSSFGASAVGLGSRRMSNSADIAIERPAPSYPVAKKSEGKILRPQYKEILRDPANSLHLIDHPPVPPNATSKEVEAYGARITRINKFKKILQATSIPLTELRDASWNGIPEEVRAMSWQLLLGYLPTSSERRVGTLERKRKEYLDGVRQAFEKGGTTSAPTGKARGLDEAIWHQISIDVPRTNPHLELYSYEATQRSLERILYVWAIRHPASGYVQGINDLVTPFWQVFLATYIADSDVESGMDPGQLPKPVLDAVEADSFWCLTKLLDGIQDNYIFAQPGIQRQVASLRDLTARIDEPLAKHLQAEGVEFIQFSFRWMNCLLMREISVQNTIRMWDTYLAEEQGFSEFHLYVCLAFLVKWSSKLLKMDFQEIMMFLQALPTRNWTETDINMLLGEAFVWQSLFKGSSSHLRGSSSTTPSSAPY\n+>EOG09262QRH\n+MASNRRQPKKPTDYNRPSGTPTPSGPAGAQAAFTSPKSGLSSDKSGNPDFSKAQDEVSKGASSQRNTVPQSEGGGAGVPNPDARKGESPDFSGKQDEFETIAADPAQAEFENKPLPDLTQGIPSTLDFELANRKSKASPLNLTEAADPEEDASGGGKGRGELPASAYVSSSERKRNQMANYMYLAFFISAITGTVYMGRNWETEEEEKLHAETAPSGWSLTGMWNRVRARTGDQLGHYTEPAFTKLLPDPSPMFERPYTLVLSMEDLLIHSEWTREHGWRLAKRPGVDYFLRYLSQYYELVIFTTQPSTLAEPVIRKFDPYHIVTWPLFREATLYENGEYIKDLSYLNRDLSKVILIDTKAHHAKKQPENAIILKPWMGDVQDKELVSLIPFLEYIPTMQYADVRKALKSFEGTHIPTEFAKREAIARKKFQEQLAEERKKHGKRGGGVGLLGSALGIKPGGMMMTDPNEQSLADALAQGKMLQDLARERGQKNYEAFDKEIRENGAKWLKEEAEMEEKAKEEGLKAMKSGMTGGWWGSSSS\n' |
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| diff -r 8e1ace8f77c6 -r 5c09ad60911c test-data/funannotate_options.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_options.loc Fri Mar 07 22:34:18 2025 +0000 |
| b |
| @@ -0,0 +1,14 @@ +# this is a tab separated file describing options available for selects in the funannotate tool +# these options are derived separetely for each funannotate DB +# +# the columns are: +# value name select db_value +# +# db_value is the ID of the funannotate DB +# value and name are the value and name to be used +# select describes the command line parameter / select for which the values can be used +insecta Insecta busco_db 2021-07-20-120000 +dikarya Dikarya busco_db 2021-07-20-120000 +fly Fly trained_species 2021-07-20-120000 +anidulans Anidulans trained_species 2021-07-20-120000 +botrytis_cinerea.dikarya botrytis_cinerea.dikarya outgroup 2021-07-20-120000 \ No newline at end of file |
| b |
| diff -r 8e1ace8f77c6 -r 5c09ad60911c tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Jun 26 09:41:06 2024 +0000 +++ b/tool_data_table_conf.xml.sample Fri Mar 07 22:34:18 2025 +0000 |
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| @@ -3,4 +3,8 @@ <columns>value, description, format_version, path</columns> <file path="tool-data/funannotate.loc" /> </table> + <table name="funannotate_options" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, select, db_value</columns> + <file path="tool-data/funannotate_options.loc" /> + </table> </tables> |
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| diff -r 8e1ace8f77c6 -r 5c09ad60911c tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Jun 26 09:41:06 2024 +0000 +++ b/tool_data_table_conf.xml.test Fri Mar 07 22:34:18 2025 +0000 |
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| @@ -3,4 +3,8 @@ <columns>value, description, format_version, path</columns> <file path="${__HERE__}/test-data/funannotate.loc" /> </table> + <table name="funannotate_options" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, select, db_value</columns> + <file path="${__HERE__}/test-data/funannotate_options.loc" /> + </table> </tables> |