| Previous changeset 4:f0606dfd5195 (2016-02-23) Next changeset 6:c5908940967d (2017-11-11) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit fc3727b1b39cd5654a523d03e0df2b9ac87ddcda |
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modified:
mafft.xml test-data/mafft_fftns_result.aln test-data/mafft_nwns_result.aln |
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| diff -r f0606dfd5195 -r 15974dd17515 mafft.xml --- a/mafft.xml Tue Feb 23 07:28:36 2016 -0500 +++ b/mafft.xml Tue Sep 20 09:30:47 2016 -0400 |
| [ |
| @@ -16,7 +16,6 @@ <![CDATA[ #if $cond_flavour.flavourType != 'custom' $cond_flavour.flavourType - #elif $cond_flavour.flavourType == 'custom' ### full parameter options mafft @@ -24,10 +23,10 @@ --retree $cond_flavour.retree --maxiterate $cond_flavour.iterations #end if - + ## specify threads to use --thread \${GALAXY_SLOTS:-1} - + $datatype --ep $ep --op $op @@ -38,12 +37,12 @@ #elif $matrix_condition.matrix == "PAM" --jtt ${matrix_condition.PAM} #end if - + $reorder - $getTree + $getTree $outputFormat $inputSequences > $outputAlignment; - + #if $getTree == "--treeout" mv ${inputSequences}.tree $outputTree; #end if |
| b |
| diff -r f0606dfd5195 -r 15974dd17515 test-data/mafft_fftns_result.aln --- a/test-data/mafft_fftns_result.aln Tue Feb 23 07:28:36 2016 -0500 +++ b/test-data/mafft_fftns_result.aln Tue Sep 20 09:30:47 2016 -0400 |
| [ |
| b"@@ -1,504 +1,504 @@\n > 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n--------------------MNGTE------------------------GDNF--------\n-YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----\n-----YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMANLFMVLFG-F\n-TVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIVICKPMGN-FR\n-FGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPDYYTLNPNFNN\n-ESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE------------------------\n----------------------------------------------------AAAAQQ---\n+--------------------------------MNGTE--------------GDNF-----\n+-------------YVP-----F-SNKTG----------LARSPYEYPQY-YLAEPWK---\n+--------------YSALAAYMFFLILVGFPVNFLTLFVTVQHKKLRTPLNYILLNLAMA\n+NLFMVLFG-FTVTMYTSMN-GYFV--FGPTMCSIEGFFATLGGEVALWSLVVLAIERYIV\n+ICKPMGN-FRFGNTHAIMGVAFTWIMALAC-AAPPLVG-W-----SRYIPEGMQCSCGPD\n+YYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTV----KE--------------\n+------------------------------------------------------AAAAQQ\n ------------------------------------------------------------\n---------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-\n-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN\n-PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------\n---------------------------------------------SPA-------------\n-------\n+--------------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVA\n+FYIFT-HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC------\n+--GKNPLGDDE--SGASTSKTEVSSVS-TSPVS---------------------------\n+-----------------------------------PA-----------------------\n+--\n > 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n--------------------MNGTE------------------------GPNF--------\n-YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----\n-----FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGG-F\n-TTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVVVCKPMSN-FR\n-FGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGIDYYTLKPEVNN\n-ESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE------------------------\n----------------------------------------------------AAAQQQ---\n+--------------------------------MNGTE--------------GPNF-----\n+-------------YVP-----F-SNITG----------VVRSPFEQPQY-YLAEPWQ---\n+--------------FSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA\n+DLFMVFGG-FTTTLYTSLH-GYFV--FGPTGCNLEGFFATLGGEIGLWSLVVLAIERYVV\n+VCKPMSN-FRFGENHAIMGVAFTWVMALAC-AAPPLVG-W-----SRYIPEGMQCSCGID\n+YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV----KE--------------\n+------------------------------------------------------AAAQQQ\n ------------------------------------------------------------\n---------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-\n-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN\n-PLGD-DE--ASATASKTE------TSQV--------------------------------\n---------------------------------------------APA-------------\n-------\n+--------------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVA\n+MYIFT-HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC------\n+--GKNPLGDDE--ASATASKTE------TSQVA---------------------------\n+-----------------------------------PA-----------------------\n+--\n > 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n--------------------MNGTE------------------------GINF--------\n-YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----\n-----YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVADLFMACFG-F\n-TVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIVVCKPMGN-FR\n-FSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPDYYTHNPDYHN\n-ESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE------------------------\n----------------------------------------------------AAAQQQ---\n+--------------------------------MNGTE--------------GINF-----\n+-------------YVP-----M-SNKTG----------VVRSPFEYPQY-YLAEPWK---\n+--------------YRLVCCYIFFLISTGLPINLLTLLVTFKHKKLRQPLNYILVNLAVA\n+DLFMACFG-FTVTFYTAWN-GYFV--FGPVGCAVEGFFATLGGQVALWSLVVLAIERYIV\n+VCKPMGN-FRFSATHAMMGIAFTWVMAFSC-AAPPLFG-W-----SRYMPEGMQCSCGPD\n+YYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKV----RE--------------\n+------------------------------------------------------AAAQQQ\n ----"..b'ITGAFLICWLPFFIIALIGPF-\n-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------\n------RGHR---------------------------------------------------\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGL----------SPTG-----\n+-------------LVTSD-----FNDSYGLTGQFINGSHSSRSRDNAS--ANDTSATNMT\n+DDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVA\n+DLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWA\n+VTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQD\n+K----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEE\n+TTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENAN\n+GVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAMLERQ-CNNGKKISSN\n+DTPYS-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIA\n+LIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFG------\n+---KY-RRGHR-------------------------------------------------\n ------------------------------------------------------------\n-------\n+--\n > 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n-MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------\n-----------LVTSDFNDSYGLTGQFINGSHSSRSRDNASANDTSATNMTDDRYWSLTVY\n-SHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVADLMVAVLV-M\n-PLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWAVTS-IDYIRR\n-RSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQDK---------\n--GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEETTLVASPKTE\n-YSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENANGVNSNSSS--\n---------SERLKQIQIETAEAFANGCA----EEASIAMLERQ-CNNGKKISSNDTPYS-\n-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIALIGPF-\n-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFGKYR---------\n------RGHR---------------------------------------------------\n+MANFTFGDLALDVARMG-----GLASTPSGLRSTGLTTPGL----------SPTG-----\n+-------------LVTSD-----FNDSYGLTGQFINGSHSSRSRDNAS--ANDTSATNMT\n+DDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAVMLERSLHNVANYLILSLAVA\n+DLMVAVLV-MPLSVVSEIS-KVWF--LHSEVCDMWISVDVLCCTASILHLVAIAMDRYWA\n+VTS-IDYIRRRSARRILLMIMVVWIVALFI-SIPPLFG-WRDP--NNDPDKTGTCIISQD\n+K----------GYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTEE\n+TTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENAN\n+GVNSNSSS----------SERLKQIQIETAEAFANGCAEEASIAMLERQ-CNNGKKISSN\n+DTPYS-------------RTREKLELK------RERKAARTLAIITGAFLICWLPFFIIA\n+LIGPF-VDPE--GIPPFARSFVLWLGYFNSLLNPIIYTIFSPEFRSAFQKILFG------\n+---KY-RRGHR-------------------------------------------------\n ------------------------------------------------------------\n-------\n+--\n > 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n--MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------\n-----------NVTVVPNTTW---------WQASAPFDTPAALVRAAAK------------\n---------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLV-M\n-PLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTN-IDYIHA\n-STAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQDV---------\n--GYQIFATASSFYVPVLIILILYWRIYQTARKRIR-------------------------\n---------------------RRRGATARGGVGPPP---------VPAGGALVAGGGSGGI\n-AAAVVAVIGRPLPTISETTTTGFTNVSS----NNTS---PEKQSCANGLEADPPTTGYGA\n-VAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLAILVPT-\n-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCGRRV---------\n------RRRRA--------------------------------------------------\n----------------------------------------------PQ-------------\n-------\n+-MEGAEGQEELDWEAL-------YLRLP--LQNCSWNSTGW----------EPNW-----\n+-------------NVTVV-----PNTTW---------WQASAPFDTPA--ALVRAAAK--\n+------------------AVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVA\n+DLLVACLV-MPLGAVYEVV-QRWT--LGPELCDMWTSGDVLCCTASILHLVAIALDRYWA\n+VTN-IDYIHASTAKRVGMMIACVWTVSFFV-CIAQLLG-WKDPDWNQRVSEDLRCVVSQD\n+V----------GYQIFATASSFYVPVLIILILYWRIYQTARKRIR---------------\n+------------------------------RRRGATARGGVGPPP---------VPAGGA\n+LVAGGGSGGIAAAVVAVIGRPLPTISETTTTGFTNVSSNNTS---PEKQSCANGLEADPP\n+TTGYGAVAAAYYPSLVRRKPKEAADSK------RERKAAKTLAIITGAFVACWLPFFVLA\n+ILVPT-CDCE---VSPVLTSLSLWLGYFNSTLNPVIYTVFSPEFRHAFQRLLCG------\n+---RR-VRRRR--A----------------------------------------------\n+-----------------------------------PQ-----------------------\n+--\n' |
| b |
| diff -r f0606dfd5195 -r 15974dd17515 test-data/mafft_nwns_result.aln --- a/test-data/mafft_nwns_result.aln Tue Feb 23 07:28:36 2016 -0500 +++ b/test-data/mafft_nwns_result.aln Tue Sep 20 09:30:47 2016 -0400 |
| b |
| b'@@ -1,270 +1,270 @@\n CLUSTAL format alignment by MAFFT NW-NS-2 (v7.221)\n \n \n-1== -------------------MNGTE------------------------GDNF--------\n-2== -------------------MNGTE------------------------GPNF--------\n-3== -------------------MNGTE------------------------GINF--------\n-4=p -------------------MNGTE------------------------GKNF--------\n-5=p -------------------MNGTE------------------------GNNF--------\n-6== -------------------MKQVPEF----------------------HEDF--------\n-7== -------------------MRKMS------------------------EEEF--------\n+1== --------------------------------MNGTE--------------GDNF-----\n+2== --------------------------------MNGTE--------------GPNF-----\n+3== --------------------------------MNGTE--------------GINF-----\n+4=p --------------------------------MNGTE--------------GKNF-----\n+5=p --------------------------------MNGTE--------------GNNF-----\n+6== --------------------------------MKQVPEF------------HEDF-----\n+7== --------------------------------MRKMS--------------EEEF-----\n 8=opsin, ------------------------------------------------------------\n-9== -------------------MAQQWSL----------QRLAGRHPQDSYEDST--------\n-10== -------------------MAQQWSL----------QRLAGRHPQDSYEDST--------\n-11== -------------------MTEAWNV----------AVFAARRSRDD-DDTT--------\n-12== -------------------MA-AWEA----------AFAARRRHEE--EDTT--------\n-13== -------------------MS---------------------------SNSS--------\n-14== ----------MESGNVSSSLFGNVST----------ALRPEARL----SA----------\n-15== ----------MEYHNVSSVL-GNVSS----------VLRPDARL----SA----------\n-16== ----------ME------PLCNASEP----------PLRPEAR-----SSGN--------\n-17== ----------MD------ALCNASEP----------PLRPEARM----SSGS--------\n-18== -------------------MTNATGP----------QMAYYGAA----SMD---------\n-19== -------------------MANVTGP----------QMAFYGSG----AAT---------\n-20== ----------ME---SFAVAAAQLGP----------HFAPLS------------------\n-21== ----------ME---SFAVAAAQLGP----------HFAPLS------------------\n-22== ----------MD---SFAAVATQLGP----------QFAAPS------------------\n-23== -----MERSHLP---ETPFDLAHSGP----------RFQAQSSG----------------\n-24== -----MERSLLP---EPPLAMALLGP----------RFEAQTGG----------------\n-25== -------------------MIAVSGP----------SYEAFSYG----GQA---------\n-26== ---------------------MANQL----------SYSSLGWP----YQP---------\n-27== ------------------------------------MVESTTLV----NQT---------\n-28== -------------------------------------MGRDLRD----NET---------\n-29== ---------MMD-------VNSSGRPDLYGHLRSF-LLPEVGRGLPDLSPDGGADPVAGS\n+9== --------------------------------MAQQWSLQRLAGRHPQDSYEDST-----\n+10== --------------------------------MAQQWSLQRLAGRHPQDSYEDST-----\n+11== --------------------------------MTEAWNVAVFAARRSRDD-DDTT-----\n+12== --------------------------------MAA-WEAAFAARRRHEE--EDTT-----\n+13== --------------------------------MS-----------------SNSS-----\n+14== ----------MES--GNV-----------SSSLFGNVSTAL----------RPEA-----\n+15== ----------MEY--HNV-----------SSVL-GNVSSVL----------RPDA-----\n+16== ----------ME-------------------PLCNASEPPL----------RPEA-----\n+17== ----------MD-------------------ALCNASEPPL----------RPEA-----\n+18== --------------------------------MTNATGPQM----------AYYG-----\n+19== --------------------------------MANVTGPQM----------AFYG-----\n+20== ---------------MES-----------FAVAAAQLGPHF----------APLS-----\n+21== ---------------MES-----------FAVAAAQLGPHF----------APLS-----\n+22== ---------------MDS-----------FAAVATQLGPQF----------AAPS-----\n+23== ------'..b'------\n-12== --------------------------------------------SPA-------------\n-13== --------------------------------------------MPAHP---V-------\n+9== -----------------------------------PA-----------------------\n+10== -----------------------------------PA-----------------------\n+11== -----------------------------------PA-----------------------\n+12== -----------------------------------PA-----------------------\n+13== -----------------------------------PAHPV--------------------\n 14== ------------------------------------------------------------\n 15== ------------------------------------------------------------\n 16== ------------------------------------------------------------\n@@ -445,52 +445,52 @@\n 24== ------------------------------------------------------------\n 25== ------------------------------------------------------------\n 26== ------------------------------------------------------------\n-27== QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA\n-28== QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA\n-29== -------------------------------------------ERPERPEFVLQNADYCR\n-30== -------------------------------------------ERPERSEFVLQNSDHCG\n-31=p -------------------------------------------ERPERSEFVLQNSDHCG\n+27== Y--PPQGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQGVDNQAY\n+28== YAPPPQGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQGVDNQAY\n+29== -----------------------------------PERPEFVL-QNADYCRKKGHDS---\n+30== -----------------------------------PERSEFVL-QNSDHCGKKGHDT---\n+31=p -----------------------------------PERSEFVL-QNSDHCGKKGHDT---\n 32== ------------------------------------------------------------\n 33=p ------------------------------------------------------------\n 34== ------------------------------------------------------------\n 35=p ------------------------------------------------------------\n-36== ---------------------------------------------PQ-------------\n+36== -----------------------------------PQ-----------------------\n \n \n-1== ------\n-2== ------\n-3== ------\n-4=p ------\n-5=p ------\n-6== ------\n-7== ------\n-8=opsin, ------\n-9== ------\n-10== ------\n-11== ------\n-12== ------\n-13== ------\n-14== ------\n-15== ------\n-16== ------\n-17== ------\n-18== ------\n-19== ------\n-20== ------\n-21== ------\n-22== ------\n-23== ------\n-24== ------\n-25== ------\n-26== ------\n-27== ------\n-28== ------\n-29== KKGHDS\n-30== KKGHDT\n-31=p KKGHDT\n-32== ------\n-33=p ------\n-34== ------\n-35=p ------\n-36== ------\n- \n+1== --\n+2== --\n+3== --\n+4=p --\n+5=p --\n+6== --\n+7== --\n+8=opsin, --\n+9== --\n+10== --\n+11== --\n+12== --\n+13== --\n+14== --\n+15== --\n+16== --\n+17== --\n+18== --\n+19== --\n+20== --\n+21== --\n+22== --\n+23== --\n+24== --\n+25== --\n+26== --\n+27== QA\n+28== QA\n+29== --\n+30== --\n+31=p --\n+32== --\n+33=p --\n+34== --\n+35=p --\n+36== --\n+ \n' |