Mercurial > repos > iuc > hyphy_fel
changeset 17:2e5ab7526bd4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
| author | iuc |
|---|---|
| date | Fri, 30 Oct 2020 16:27:01 +0000 |
| parents | af7490b6329b |
| children | c32f3d3e8a92 |
| files | hyphy_fel.xml macros.xml test-data/slac-out1.json |
| diffstat | 3 files changed, 2035 insertions(+), 2035 deletions(-) [+] |
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--- a/hyphy_fel.xml Fri Sep 18 21:09:33 2020 +0000 +++ b/hyphy_fel.xml Fri Oct 30 16:27:01 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> +<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0" profile="19.09"> <description>Fixed Effects Likelihood</description> <macros> <import>macros.xml</import>
--- a/macros.xml Fri Sep 18 21:09:33 2020 +0000 +++ b/macros.xml Fri Oct 30 16:27:01 2020 +0000 @@ -107,14 +107,14 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.17</token> + <token name="@VERSION@">2.5.21</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> - <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> + <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> <token name="@CATCH_MPIERR@"><![CDATA[ EC=\$? ; if [ \$EC -ne 0 ] ; then
--- a/test-data/slac-out1.json Fri Sep 18 21:09:33 2020 +0000 +++ b/test-data/slac-out1.json Fri Oct 30 16:27:01 2020 +0000 @@ -1,876 +1,28 @@ { - "analysis":{ - "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", - "version":"2.00", - "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", - "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", - "contact":"spond@temple.edu", - "requirements":"in-frame codon alignment and a phylogenetic tree" - }, - "fits":{ - "Nucleotide GTR":{ - "Log Likelihood":-3531.963798530155, - "estimated parameters":24, - "AIC-c":7112.142458295762, - "Equilibrium frequencies":[ - [0.3563279857397504], - [0.1837789661319073], - [0.2402852049910873], - [0.2196078431372549] - ], - "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714, - "Substitution rate from nucleotide A to nucleotide G":1, - "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238, - "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331, - "Substitution rate from nucleotide C to nucleotide T":1.018028772244997, - "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378 - }, - "display order":0 - }, - "Global MG94xREV":{ - "Log Likelihood":-3466.724829119623, - "estimated parameters":31, - "AIC-c":6996.52909240682, - "Equilibrium frequencies":[ - [0.04785168648208005], - [0.03911346079312019], - [0.04842054060317301], - [0.04069665666515385], - [0.01817010744778396], - [0.01485205303123071], - [0.01838611113045968], - [0.01545321970309948], - [0.0190138898893362], - [0.01554175184587827], - [0.01923992433904378], - [0.01617083546230154], - [0.02796925133965702], - [0.02286176927319543], - [0.02830174586718859], - [0.02378714529482007], - [0.01687870337957799], - [0.01379647304851128], - [0.01707935503225849], - [0.01435491300079667], - [0.006409133648843443], - [0.005238757839512795], - [0.006485324528555602], - [0.005450807083377185], - [0.006706760641638982], - [0.005482034985409045], - [0.006786489669196017], - [0.005703931360295163], - [0.009865581170012171], - [0.008064021368173151], - [0.009982861811889655], - [0.008390428826966174], - [0.03287895020631181], - [0.02687490503171972], - [0.033269810543681], - [0.0279627207822247], - [0.01248470225271473], - [0.01020486315060615], - [0.01263311863778268], - [0.01061792547971484], - [0.01306446616325414], - [0.01067875601941112], - [0.01321977470017749], - [0.01111100011404158], - [0.01921770557551369], - [0.01570834862514353], - [0.01944616295744266], - [0.01634417558076203], - [0.01975257768318274], - [0.02055210293142003], - [0.009176034326710849], - [0.007500393094996483], - [0.00928511773266342], - [0.007803986567571961], - [0.00784869593340758], - [0.009716299514778986], - [0.008166387662818644], - [0.01412467213650941], - [0.01154535713247913], - [0.01429258425298098], - [0.01201267864744234] - ], - "Rate Distributions":{ - "non-synonymous/synonymous rate ratio for *test*":[ - [0.9952474740528205, 1] - ] - }, - "display order":1 - } - }, - "timers":{ - "Total time":{ - "timer":62, - "order":0 - }, - "Model fitting":{ - "timer":12, - "order":1 - }, - "Primary SLAC analysis":{ - "timer":1, - "order":2 - }, - "Ancestor sampling analysis":{ - "timer":31, - "order":3 - } - }, - "tested":{ - "0":{ - "Pig":"test", - "Cow":"test", - "Node3":"test", - "Horse":"test", - "Cat":"test", - "Node2":"test", - "RhMonkey":"test", - "Baboon":"test", - "Node9":"test", - "Human":"test", - "Chimp":"test", - "Node12":"test", - "Node8":"test", - "Node1":"test", - "Rat":"test", - "Mouse":"test" - } - }, - "input":{ - "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta", - "number of sequences":10, - "number of sites":187, - "partition count":1, - "trees":{ - "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" - } - }, - "data partitions":{ - "0":{ - "name":"slac.filter.default", - "coverage":[ - [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] - ] - } - }, - "branch attributes":{ - "0":{ - "Human":{ - "original name":"Human", - "Nucleotide GTR":0, - "Global MG94xREV":0, - "codon":[ - ["AAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", 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1.725289655759397], + [0.566048512190645, 2.433951487809356, 2, 3, 0.1886828373968816, 3.533266066295039, 1.232563596696871, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] ] } } + }, + "headers": [ +["ES", "Expected synonymous sites"], + ["EN", "Expected non-synonymous sites"], + ["S", "Inferred synonymous substitutions"], + ["N", "Inferred non-synonymous substitutions"], + ["P[S]", "Expected proportion of synonymous sites"], + ["dS", "Inferred synonymous susbsitution rate"], + ["dN", "Inferred non-synonymous susbsitution rate"], + ["dN-dS", "Scaled by the length of the tested branches"], + ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with P<sub>s</sub> probability of success"], + ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with P<sub>s</sub> probability of success"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "Global MG94xREV":0.001710698008755675, + "Nucleotide GTR":0.001679501710016974, + "amino-acid": [ +["K", "E", "I", "R", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "D", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "K", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "E", "E", "K", "D", "A", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "I", "H", "D", "Q", "D", "S", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "T", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "E", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", 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GTR":0.2660443541848668, + "amino-acid": [ +["-", "-", "-", "A", "N", "D", "D", "I", "V", "W", "G", "T", "L", "G", "Q", "D", "I", "N", "L", "D", "I", "P", "D", "S", "Q", "-", "G", "I", "N", "I", "D", "D", "I", "H", "W", "E", "K", "-", "-", "G", "K", "K", "K", "V", "A", "R", "F", "Q", "I", "S", "N", "K", "P", "K", "N", "P", "D", "E", "K", "Y", "N", "V", "S", "M", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "M", "L", "E", "D", "C", "D", "T", "Y", "K", "V", "V", "I", "Y", "D", "K", "D", "G", "K", "N", "V", "L", "D", "K", "T", "F", "Q", "L", "K", "I", "Q", "E", "K", "V", "S", "T", "P", "N", "I", "D", "W", "N", "C", "I", "N", "K", "T", "L", "V", "C", "K", "V", "S", "N", "G", "T", "D", "P", "E", "L", "K", "L", "Y", "V", "N", "G", "T", "S", "I", "K", "P", "V", "S", "S", "K", "F", "S", "T", "Y", "R", "F", "I", "N", "K", "Q", "K", "I", "L", "V", "N", "C", "T", "A", "E", "N", "K", "V", "S", "K", "E", "S", "D", "V", "K", "M", "I", "T", "C", "S", "E", "K", "G", "L", "D"] + ], + "codon": [ 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"timer":14 + } } } \ No newline at end of file