| Next changeset 1:5e48c4621f9f (2015-07-31) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 1fc2105007248c6b9460c0f3a98e6589477d0b13 |
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added:
mafft.xml test-data/mafft_fftns_result.aln test-data/mafft_nwns_result.aln test-data/sample.fa tool_dependencies.xml |
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| diff -r 000000000000 -r a4e086689fae mafft.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mafft.xml Thu Jun 18 08:59:56 2015 -0400 |
| [ |
| @@ -0,0 +1,152 @@ +<tool id="rbc_mafft" name="MAFFT" version="7.221.0"> + <description>Multiple alignment program for amino acid or nucleotide sequences</description> + <requirements> + <requirement type="package" version="7.221">mafft</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> + </stdio> + <version_command> + <![CDATA[ + mafft --version + ]]> + </version_command> + <command> + <![CDATA[ + #if $cond_flavour.flavourType != 'custom' + $cond_flavour.flavourType + #elif $cond_flavour.flavourType == 'custom' + ### full parameter options + mafft + #end if + + ## specify threads to use + --thread \${GALAXY_SLOTS:-1} + + #if $outputFormat.value == 'clustalw' + --clustalout + #end if + + $inputSequences > + + #if $outputFormat.value == 'fasta' + $outputFasta + #elif $outputFormat.value == 'clustalw' + $outputClustalW + #end if + ]]> + </command> + <inputs> + <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> + <conditional name="cond_flavour"> + <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section."> + <option value="mafft-fftns" selected="true">fftns</option> + <option value="mafft-fftnsi">fftnsi</option> + <option value="mafft-nwns">nwns</option> + <option value="mafft-nwnsi">nwnsi</option> + <option value="mafft-einsi">einsi</option> + <option value="mafft-ginsi">ginsi</option> + <option value="mafft-linsi">linsi</option> + <option value="mafft-qinsi">qinsi</option> + <option value="mafft-xinsi">xinsi</option> + <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters --> + </param> + <when value="mafft-fftns"/> + <when value="mafft-fftnsi"/> + <when value="mafft-nwns"/> + <when value="mafft-nwnsi"/> + <when value="mafft-einsi"/> + <when value="mafft-ginsi"/> + <when value="mafft-linsi"/> + <when value="mafft-qinsi"/> + <when value="mafft-xinsi"/> + </conditional> + <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW"> + <option value="fasta" selected="true">FASTA</option> + <option value="clustalw">ClustalW</option> + </param> + </inputs> + <outputs> + <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}"> + <filter>outputFormat == 'fasta'</filter> + </data> + <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}"> + <filter>outputFormat == 'clustalw'</filter> + </data> + </outputs> + <tests> + <test> + <param name="inputSequences" value="sample.fa"/> + <param name="flavourType" value="mafft-fftns"/> + <param name="outputFormat" value="fasta"/> + <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/> + </test> + <test> + <param name="inputSequences" value="sample.fa"/> + <param name="flavourType" value="mafft-nwns"/> + <param name="outputFormat" value="clustalw"/> + <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/> + </test> + </tests> + <help> + <![CDATA[ +**What it does** + +MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), +FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. + +From the MAFFT man page, an overview of the different predefined flavours of the tool. + +**Accuracy-oriented methods:** + +- L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): + + - mafft --localpair --maxiterate 1000 input [> output] + +- G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): + + - mafft --globalpair --maxiterate 1000 input [> output] + +- E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): + + - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps. + + +**Speed-oriented methods:** + +- FFT-NS-i (iterative refinement method; two cycles only): + + - mafft --retree 2 --maxiterate 2 input [> output] + +- FFT-NS-i (iterative refinement method; max. 1000 iterations): + + - mafft --retree 2 --maxiterate 1000 input [> output] + +- FFT-NS-2 (fast; progressive method): + + - mafft --retree 2 --maxiterate 0 input [> output] + +- FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): + + - mafft --retree 1 --maxiterate 0 input [> output] + +- NW-NS-i (iterative refinement method without FFT approximation; two cycles only): + + - mafft --retree 2 --maxiterate 2 --nofft input [> output] + +- NW-NS-2 (fast; progressive method without the FFT approximation): + + - mafft --retree 2 --maxiterate 0 --nofft input [> output] + +- NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): + + - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] + + ]]> + </help> + <citations> + <citation type="doi">10.1093/molbev/mst010</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r a4e086689fae test-data/mafft_fftns_result.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_fftns_result.aln Thu Jun 18 08:59:56 2015 -0400 |
| [ |
| b"@@ -0,0 +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+------------------------------------------------------------\n+--------------ESASTQK------AEKEVTRMVVLMVIGFLVCWVPYASVAFYIFT-\n+HQGS--DFGATFMTLPAFFAKSSALYNPVIYILMNKQFRNCMITTLCC---------GKN\n+PLGD-DE--SGASTSKTEVSSVS-TSPV--------------------------------\n+--------------------------------------------SPA-------------\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+------------------------------------------------------------\n+--------------ESATTQK------AEKEVTRMVIIMVIFFLICWLPYASVAMYIFT-\n+HQGS--NFGPIFMTLPAFFAKTASIYNPIIYIMMNKQFRNCMLTSLCC---------GKN\n+PLGD-DE--ASATASKTE------TSQV--------------------------------\n+--------------------------------------------APA-------------\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+------------------------------------------------------------\n+--------------ESATTQK------AEKEVTRMVILMVLGFMLAWTPYAVVAFWIFT-\n+NKGA--DFTATLMAVPAFFSKSSSLYNPIIYVLMNKQFRNCMITTICC---------GKN\n+PFGD-EDVSSTVSQSKTEVSSVS-SSQV--------------------------------\n+--------------------------------------------SPA-------------\n+------\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+-------------------MNGTE------------------------GKNF--------\n+YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----\n+----FKILALYLFFLMSMGLPINGLTLVVTAQHKKLRQPLNFILVNLAVAGTIMVCFG-F\n+TVTFYTAIN-GYFV--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK\n+FSSSHAFAGIAFTWVMALAC-AAPPLFG-W-----SRYIPEGMQCSCGPDYYTLNPDYNN\n+ESYVIYMFVCHFILPVAVIFFTYGRLVCTV----KA------------------------\n+---------------------------------------------------AAAQQQ---\n+------------------------------------------------------------\n+--------------DSASTQK------AEREVTKMVILMVFGFLIAWTPYATVAAWIFF-\n+NKGA--DFSAKFMAIPAFFSKSSALYNPVIYVLLNKQFRNCMLTTIFC---------GKN\n+PLGD-DE-SSTVSTSKTEVSS------V--------------------------------\n+--------------------------------------------SPA-------------\n+------\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+-------------------MNGTE------------------------GNNF--------\n+YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----\n+----FKLLAVYMFFLICLGLPINGLTLICTAQHKKLRQPLNFILVNLAVAGAIMVCFG-F\n+TVTFYTAIN-GYFA--LGPTGCAVEGFMATLGGEVALWSLVVLAIERYIVVCKPMGS-FK\n+FSSTHASAGIAFTWVMAMAC-AAPPLVG-W-----SRYIPEGIQCSCGPDYYTLNPEYNN\n+ESYVLYMFICHFILPVTIIFFTYGRLVCTV----KA------------------------\n+---------------------------------------------------AAAQQQ---\n+------------------------------------------------------------\n+--------------DSASTQK------AEREVTKMVILMVLGFLVAWTPYATVAAWIFF-\n+NKGA--AFSAQFMAIPAFFSKTSALYNPVIYVLLNKQFRSCMLTTLFC--"..b"TGG--------\n+----------NTTGISDVTV----------------------------------------\n+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L\n+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK\n+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------\n+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------\n+---------------TVKKVEKTGADTRHGASPAPQPKKS-----------VNGESGSR-\n+--------NWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAG-\n+-PTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-\n+CESSC-HMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------\n+-----RQ-----------------------------------------------------\n+------------------------------------------------------------\n+------\n+> 33=p A35181 serotonin receptor class 1A - rat\n+----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------\n+----------NVTSISDVTF----------------------------------------\n+--SYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLV-L\n+PMAALYQVL-NKWT--LGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK\n+RTPRRAAALISLTWLIGFLI-SIPPMLG-WRTPEDRSDPDA---CTISKDH---------\n+-GYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK------------------------\n+---------------TVRKVEKKGAGTSLGTSSAPPPKKS-----------LNGQPGSG-\n+--------DWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGNSKEHLPLPSESG-\n+-SNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPF-\n+CESSC-HMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC---------\n+-----RR-----------------------------------------------------\n+------------------------------------------------------------\n+------\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\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+------------------------------------------------------------\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+------------------------------------------------------------\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" |
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| diff -r 000000000000 -r a4e086689fae test-data/mafft_nwns_result.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mafft_nwns_result.aln Thu Jun 18 08:59:56 2015 -0400 |
| b |
| b'@@ -0,0 +1,496 @@\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+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+30== ------------------------------------------------------------\n+31=p ------------------------------------------------------------\n+32== ----------MD-------VLSPG------------QGNNTTSPPAPFETGG--------\n+33=p ----------MD-------VFSFG------------QGNNTTASQEPFGTGG--------\n+34== MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------\n+35=p MANFTFGDLALD-------VARMG-----GLASTPSGLRSTGLTTPGLSPTG--------\n+36== -MEGAEGQEELD-------WEAL-------YLRLP--LQNCSWNSTGWEPNW--------\n+ \n+\n+1== YVP----F-SNKTGLARSPY----------------EYPQY-------YLAEPWK-----\n+2== YVP----F-SNITGVVRSPF----------------EQPQY-------YLAEPWQ-----\n+3== YVP----M-SNKTGVVRSPF----------------EYPQY-------YLAEPWK-----\n+4=p YVP----M-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----\n+5=p YVP----L-SNRTGLVRSPF----------------EYPQY-------YLAEPWQ-----\n+6== YIPIPLDI-NNLS--AYSPF----------------LVPQD-------HLGNQGI-----\n+7== YL-----F-KNIS--SVGPW----------------DGPQY-------HIAPVWA-----\n+8=opsin, ------------------------------------------------------------\n+9== QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----\n+10== QSSI-FTY-TNSNS-TRGPF----------------EGPNY-------HIAPRWV-----\n+11== RGSV-FTY-TNTNN-TRGPF----------------EGPNY-------HIAPRWV-----\n+12== RDSV-FTY-TNSNN-TRGPF----------------EGPNY-------HIAPRWV-----\n+13== QAP--------PNG-TPGPF----------------DGPQW------PYQAPQST-----\n+14== -ETRLL'..b' -----RGHR---------------------------------------------------\n+36== -----RRRRA--------------------------------------------------\n+ \n+\n+1== --------------------------------------------SPA-------------\n+2== --------------------------------------------APA-------------\n+3== --------------------------------------------SPA-------------\n+4=p --------------------------------------------SPA-------------\n+5=p --------------------------------------------SPA-------------\n+6== --------------------------------------------APEK------------\n+7== --------------------------------------------GPN-------------\n+8=opsin, ------------------------------------------------------------\n+9== --------------------------------------------SPA-------------\n+10== --------------------------------------------SPA-------------\n+11== --------------------------------------------APA-------------\n+12== --------------------------------------------SPA-------------\n+13== --------------------------------------------MPAHP---V-------\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== QGYPPQGAYPPPQGYPPQGYPPQGYPPQGYPPQGAPPQVEAPQGAPPQG---VDNQAYQA\n+28== QGYPPQGY--PPQGYPPQGYPPQGYPP---PPQGAPPQ-GAPPAAPPQG---VDNQAYQA\n+29== -------------------------------------------ERPERPEFVLQNADYCR\n+30== -------------------------------------------ERPERSEFVLQNSDHCG\n+31=p -------------------------------------------ERPERSEFVLQNSDHCG\n+32== ------------------------------------------------------------\n+33=p ------------------------------------------------------------\n+34== ------------------------------------------------------------\n+35=p ------------------------------------------------------------\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' |
| b |
| diff -r 000000000000 -r a4e086689fae test-data/sample.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.fa Thu Jun 18 08:59:56 2015 -0400 |
| [ |
| b"@@ -0,0 +1,285 @@\n+> 1== M63632 1 Lampetra japonica rhodopsin <>[BBRC174,1125-1132'91]\n+MNGTEGDNFYVPFSNKTGLARSPYEYPQYYLAEPWKYSALAAYMFFLILVGFPVNFLTLF\n+VTVQHKKLRTPLNYILLNLAMANLFMVLFGFTVTMYTSMNGYFVFGPTMCSIEGFFATLG\n+GEVALWSLVVLAIERYIVICKPMGNFRFGNTHAIMGVAFTWIMALACAAPPLVGWSRYIP\n+EGMQCSCGPDYYTLNPNFNNESYVVYMFVVHFLVPFVIIFFCYGRLLCTVKEAAAAQQES\n+ASTQKAEKEVTRMVVLMVIGFLVCWVPYASVAFYIFTHQGSDFGATFMTLPAFFAKSSAL\n+YNPVIYILMNKQFRNCMITTLCCGKNPLGDDESGASTSKTEVSSVSTSPVSPA\n+> 2== U22180 1 rat opsin <rod>[J.Mol.Neurosci.5(3),207-209'94]\n+MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY\n+VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG\n+GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP\n+EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES\n+ATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTLPAFFAKTASI\n+YNPIIYIMMNKQFRNCMLTSLCCGKNPLGDDEASATASKTETSQVAPA\n+> 3== M92038 1 chicken green sensitive cone opsin <retina>[PNAS89,5932-5936'9\n+MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL\n+VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG\n+GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWSRYMP\n+EGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKVREAAAQQQES\n+ATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAVPAFFSKSSSL\n+YNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSSQVSPA\n+> 4=p A45229 opsin, green-sensitive (clone GFgr-1) - goldfish\n+MNGTEGKNFYVPMSNRTGLVRSPFEYPQYYLAEPWQFKILALYLFFLMSMGLPINGLTLV\n+VTAQHKKLRQPLNFILVNLAVAGTIMVCFGFTVTFYTAINGYFVLGPTGCAVEGFMATLG\n+GEVALWSLVVLAIERYIVVCKPMGSFKFSSSHAFAGIAFTWVMALACAAPPLFGWSRYIP\n+EGMQCSCGPDYYTLNPDYNNESYVIYMFVCHFILPVAVIFFTYGRLVCTVKAAAAQQQDS\n+ASTQKAEREVTKMVILMVFGFLIAWTPYATVAAWIFFNKGADFSAKFMAIPAFFSKSSAL\n+YNPVIYVLLNKQFRNCMLTTIFCGKNPLGDDESSTVSTSKTEVSSVSPA\n+> 5=p B45229 opsin, green-sensitive (clone GFgr-2) - goldfish\n+MNGTEGNNFYVPLSNRTGLVRSPFEYPQYYLAEPWQFKLLAVYMFFLICLGLPINGLTLI\n+CTAQHKKLRQPLNFILVNLAVAGAIMVCFGFTVTFYTAINGYFALGPTGCAVEGFMATLG\n+GEVALWSLVVLAIERYIVVCKPMGSFKFSSTHASAGIAFTWVMAMACAAPPLVGWSRYIP\n+EGIQCSCGPDYYTLNPEYNNESYVLYMFICHFILPVTIIFFTYGRLVCTVKAAAAQQQDS\n+ASTQKAEREVTKMVILMVLGFLVAWTPYATVAAWIFFNKGAAFSAQFMAIPAFFSKTSAL\n+YNPVIYVLLNKQFRSCMLTTLFCGKNPLGDEESSTVSTSKTEVSSVSPA\n+> 6== L11864 1 Carassius auratus blue cone opsin <retina>[Biochemistry32,208-\n+MKQVPEFHEDFYIPIPLDINNLSAYSPFLVPQDHLGNQGIFMAMSVFMFFIFIGGASINI\n+LTILCTIQFKKLRSHLNYILVNLSIANLFVAIFGSPLSFYSFFNRYFIFGATACKIEGFL\n+ATLGGMVGLWSLAVVAFERWLVICKPLGNFTFKTPHAIAGCILPWISALAASLPPLFGWS\n+RYIPEGLQCSCGPDWYTTNNKYNNESYVMFLFCFCFAVPFGTIVFCYGQLLITLKLAAKA\n+QADSASTQKAEREVTKMVVVMVLGFLVCWAPYASFSLWIVSHRGEEFDLRMATIPSCLSK\n+ASTVYNPVIYVLMNKQFRSCMMKMVCGKNIEEDEASTSSQVTQVSSVAPEK\n+> 7== M13299 1 human BCP <>[Science232(4747),193-202'86]\n+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL\n+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV\n+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL\n+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT\n+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP\n+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN\n+> 8=opsin, greensensitive human (fragment) S07060\n+DLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKP\n+FGNVRFDAKLAIVGIAFSWIWAAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQS\n+YMIVLMVTCCITPLSIIVLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFC\n+> 9== K03494 1 human GCP <>[Science232(4747),193-202'86]\n+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n+IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV\n+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA\n+AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL\n+QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH\n+PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS\n+VSPA\n+> 10== Z68193 1 human Red Opsin <>[]\n+MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM\n+IFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFV\n+LGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWS\n+AVWTAPPIFGWSRYWPH"..b"ISIDR\n+YLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGWAQNVNDDKVCLISQDFGYT\n+IYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRVEPDSVIALNGIVKLQKEVE\n+ECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWLPFFLLSTARPFICGTSCSC\n+IPLWVERTFLWLGYANSLINPFIYAFFNRDLRTTYRSLLQCQYRNINRKLSAAGMHEALK\n+LAERPERPEFVLQNADYCRKKGHDS\n+> 30== L15228 1 rat 5HT-7 serotonin receptor <>[JBC268,18200-18204'93]\n+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRPTSRSLLQC\n+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n+> 31=p A47425 serotonin receptor 5HT-7 - rat\n+MPHLLSGFLEVTASPAPTWDAPPDNVSGCGEQINYGRVEKVVIGSILTLITLLTIAGNCL\n+VVISVSFVKKLRQPSNYLIVSLALADLSVAVAVMPFVSVTDLIGGKWIFGHFFCNVFIAM\n+DVMCCTASIMTLCVISIDRYLGITRPLTYPVRQNGKCMAKMILSVWLLSASITLPPLFGW\n+AQNVNDDKVCLISQDFGYTIYSTAVAFYIPMSVMLFMYYQIYKAARKSAAKHKFPGFPRV\n+QPESVISLNGVVKLQKEVEECANLSRLLKHERKNISIFKREQKAATTLGIIVGAFTVCWL\n+PFFLLSTARPFICGTSCSCIPLWVERTCLWLGYANSLINPFIYAFFNRDLRTTYRSLLQC\n+QYRNINRKLSAAGMHEALKLAERPERSEFVLQNSDHCGKKGHDT\n+> 32== M83181 1 human serotonin receptor <>[JBC267(11),7553-7562'92]\n+MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAA\n+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADT\n+RHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGN\n+SKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n+FFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n+RQ\n+> 33=p A35181 serotonin receptor class 1A - rat\n+MDVFSFGQGNNTTASQEPFGTGGNVTSISDVTFSYQVITSLLLGTLIFCAVLGNACVVAA\n+IALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCC\n+TSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPED\n+RSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVRKVEKKGAGT\n+SLGTSSAPPPKKSLNGQPGSGDWRRCAENRAVGTPCTNGAVRQGDDEATLEVIEVHRVGN\n+SKEHLPLPSESGSNSYAPACLERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLP\n+FFIVALVLPFCESSCHMPALLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFC\n+RR\n+> 34== L06803 1 Lymnaea stagnalis serotonin receptor <>[PNAS90,11-15'93]\n+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n+NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n+> 35=p A47174 serotonin receptor, 5HTlym receptor - great pond snail\n+MANFTFGDLALDVARMGGLASTPSGLRSTGLTTPGLSPTGLVTSDFNDSYGLTGQFINGS\n+HSSRSRDNASANDTSATNMTDDRYWSLTVYSHEHLVLTSVILGLFVLCCIIGNCFVIAAV\n+MLERSLHNVANYLILSLAVADLMVAVLVMPLSVVSEISKVWFLHSEVCDMWISVDVLCCT\n+ASILHLVAIAMDRYWAVTSIDYIRRRSARRILLMIMVVWIVALFISIPPLFGWRDPNNDP\n+DKTGTCIISQDKGYTIFSTVGAFYLPMLVMMIIYIRIWLVARSRIRKDKFQMTKARLKTE\n+ETTLVASPKTEYSVVSDCNGCNSPDSTTEKKKRRAPFKSYGCSPRPERKKNRAKKLPENA\n+NGVNSNSSSSERLKQIQIETAEAFANGCAEEASIAMLERQCNNGKKISSNDTPYSRTREK\n+LELKRERKAARTLAIITGAFLICWLPFFIIALIGPFVDPEGIPPFARSFVLWLGYFNSLL\n+NPIIYTIFSPEFRSAFQKILFGKYRRGHR\n+> 36== X95604 1 Bombyx mori serotonin receptor <antennae>[InsectBiochem.Mol.Bi\n+MEGAEGQEELDWEALYLRLPLQNCSWNSTGWEPNWNVTVVPNTTWWQASAPFDTPAALVR\n+AAAKAVVLGLLILATVVGNVFVIAAILLERHLRSAANNLILSLAVADLLVACLVMPLGAV\n+YEVVQRWTLGPELCDMWTSGDVLCCTASILHLVAIALDRYWAVTNIDYIHASTAKRVGMM\n+IACVWTVSFFVCIAQLLGWKDPDWNQRVSEDLRCVVSQDVGYQIFATASSFYVPVLIILI\n+LYWRIYQTARKRIRRRRGATARGGVGPPPVPAGGALVAGGGSGGIAAAVVAVIGRPLPTI\n+SETTTTGFTNVSSNNTSPEKQSCANGLEADPPTTGYGAVAAAYYPSLVRRKPKEAADSKR\n+ERKAAKTLAIITGAFVACWLPFFVLAILVPTCDCEVSPVLTSLSLWLGYFNSTLNPVIYT\n+VFSPEFRHAFQRLLCGRRVRRRRAPQ\n" |
| b |
| diff -r 000000000000 -r a4e086689fae tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jun 18 08:59:56 2015 -0400 |
| b |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mafft" version="7.221"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/MAFFT/mafft-7.221-with-extensions-src.tgz</action> + <action type="change_directory">./core</action> + <action type="shell_command">sed -i "s|\(PREFIX = \).*$|\1$INSTALL_DIR|" Makefile</action> + <action type="shell_command">make clean; make; make install</action> + <action type="change_directory">../extensions</action> + <action type="shell_command">sed -i "s|\(PREFIX = \).*$|\1$INSTALL_DIR|" Makefile</action> + <action type="shell_command">make clean; make; make install</action> + <action type="set_environment"> + <environment_variable name="MAFFT_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency> |