diff test-data/input_ncbi.faa @ 0:a968af0a91f9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_ncbi.faa	Fri May 26 09:19:12 2023 +0000
@@ -0,0 +1,74 @@
+>blaTEM-156
+MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLS
+RVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRL
+DRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS
+RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
+>blaPDC-114_blast BLAST (100% length, but 1 mismatch)
+MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
+TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALVGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
+YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
+PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
+QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
+>blaOXA-436_partial (Should be partial OXA-48 family
+MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIA
+LDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDG
+GIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVW
+>vanG
+MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKN
+LCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGENGTLQGIFELAGIPVVGCDTLSSALCMDK
+DRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAF
+EHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQ
+EAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE
+>gyrA  T86I  Campylobacter
+MENIFSKDSDIELVDIENSIKGSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMQNDEAKSRTDFVKSARIVGAVIGRYHPHGDAAVYDALVRMAQDFSMRYPSITGQGNFGSIDGDSAAAMRYTEAKMSKLSHELLKD
+IDKDTVDFVPNYDGSESEPDVLPSRVPNLLLNGSSGIAVGMATNIPPHSLNELIDGLLYLLDSKDASLEE
+IMQFIKGPDFPTGGIIYGKKGIIEAYRTGRGRVKVRAKTHIEKKTNKDVIVIDELPYQTNKARLIEQIAE
+LVKEKQIEGISEVRDESNKEGIRVVIELKREAMSEIVLNNLFKSTTMESTFGVIMLAIHNKEPKIFSLLE
+LLNLFLTHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKNSSDNNTARDSLVAKFGLSEL
+QANAILDMKLGRLTGLEREKIENELAELMKEIARLEEILKSETLLENLIRDELKEIRSKFDVPRITQIED
+DYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFV
+TDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQAEEKIMAIIPTTDFDESKSLCFFTKNGIVKRTNLSEY
+QNIRSVGVRAINLDENDELVTAIIVQRDEDEIFATGGEENLENQEIENLDDENLENEESVSTQGKMLFAV
+TKKGMCIKFPLAKVREIGRVSRGVTAIKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQS
+RGGKGVICMKLTEKTKDLISVVIVDETMDLMALTSSGKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSI
+AKCPKEENDEDELSDENFGLDL
+>50S_L22 Campylobacter 50S_L22:A103V
+MSKALIKFIRLSSTKARLIAREVQGMNAELAMASLKFMPNKGAKYIANAISSAVANGGFEANEVIVKSCRVDAAAVLKRF
+RPRARGSASRIRKPTSHILVEVVKAEVKAEEKKTVAKKTTTTKAPAKKTTSTKKATAKKES
+
+>nimIJ_hmm  WP_027455679.1 NimIJ family nitroimidazole resistance protein [Prevotella brevis]
+MSEFREMRRKRQQLTDADSIAVLQKATSGTLALLGDNDYPYAVPISYVYDNGKLYFHSAMAGHKVDAIRR
+CNKASFCVIEKDDVRPEKYTTYFRSVIAFGRIEIVEDEAEKRTIMHMMGNRFNPNHDDALQKELESGLAH
+MLAIRMDIEHLTGKEAIELVRQRGGN
+
+>aph3pp-Ib_partial_5p_neg  NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence  2160922-2162737  150-1527  704-137
+IRKLKEPPLNRTNIFFGESHSDWLPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKGRGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLSVDQCPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDMVVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADL
+
+>sul2_partial_3p_neg   NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence  2160922-2162737  150-1377  2-667
+SSNPDAAPVSSDTEIERIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR
+
+>blaTEM-internal_stop
+HFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVNYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSCVDAG
+QEQLGRSIHYSQNDLVEYSPVTEKHLTDGMTLRELCSAAITMSDNTAANLLLTTIGGPKELTA
+
+>qacR-curated_blast  (ADK23698.1)
+MKLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQI
+KCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEW
+CINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK
+
+>arsR-suppressed-in-escherichia BAE77793.1  arsR_K-12 As(III)-sensing_metalloregulatory_transcriptional_repressor_ArsR
+MSFLLPIQLFKILADETRLGIVLLLSELGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAW
+AAKIIDEAWRCEQEKVQAIVRNLARQNCSGDSKNICS
+
+>emrD3-suppressed-in-vibrio ABQ18953.1
+MKTKPSLWLMVIMLMFPQIVETIYSPVLGSIARSFSVSDAQAAQTLSVYFLAFALGVVIWGVLADKWGRRPTMLVGLLIY
+GSATFIAMQTDSFTILMLARVFSAFGIAVGSVVTQTILRDVFSGHELRKVFSLMGIGISISPVLGMLLGGQLAFAGGHQL
+VFLALFFIALVLFVYNLCQLPETQQVKPKIALGCLVARMFKDRQVLLSALLVALYNVALFSYYQLGAFIFSDLGLDAEQF
+GYSGIALGLGSLIGSFLNKTLLAKQVPQRALLLLAALLLIMGTIGVSLTLDSIGFVAAMILVVIAYGMAIPNILSTALVE
+YKSQAGSAGALFGLLYYLLIGSGLALTGLVQRLGVVLLMCAGITLLATLARSSHIARLP
+
+>pmrB_C84R
+MHFLRRPISLRQRLILTIGAILLVFELISVFWLWHESTEQIQLFEQALRDNRNNDRHIMREIREAVASLIVPGVFMVSLTLFIRYQAVRRITRPLAELQKELEARTADNLTPIAIHSATLEIEAVVSALNDLVSRLTSTLDNERLFTADVAHELRTPLAGVRLHLELLAKTHHIDVAPLVARLDQMMESVSQLLQLARAGQSFSSGNYQHVKLLEDVILPSYDELSTMLDQRQQTLLLPESAADITVQGDATLLRMLLRNLVENAHRYSPQGSNIMIKLQEDDGAVMAVEDEGPGIDESKCGELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQETSGTRAWVRLKKDQYVANQI
+
+>nfsA_R15C_K141STOP
+MTPTIELICGHRSICHFTDEPISEAQREAIINSARATSSSSFLQYSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVT