diff test-data/busted-out1.json @ 0:551616a65f8f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busted-out1.json	Wed Aug 21 12:24:55 2019 -0400
@@ -0,0 +1,361 @@
+{
+ "analysis":{
+   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",
+   "version":"1.2",
+   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
+   "authors":"Sergei L Kosakovsky Pond",
+   "contact":"[e-mail]",
+   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
+  },
+ "input":{
+   "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",
+   "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)"
+    }
+  },
+ "background":0,
+ "fits":{
+   "Nucleotide GTR":{
+     "Log Likelihood":-3531.963798530155,
+     "estimated parameters":24,
+     "AIC-c":7112.142458295762,
+     "Equilibrium frequencies":[
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+      [0.1837789661319073],
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+      [0.2196078431372549]
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+     "Rate Distributions":{
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+       "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
+    },
+   "MG94xREV with separate rates for branch sets":{
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+     "AIC-c":6996.530451399855,
+     "Equilibrium frequencies":[
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+     "AIC-c":6945.751768776152,
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+   "Constrained model":{
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+     "Rate Distributions":{
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+   "optimized null":[
+    [-9.984891074365004, -3.552861592101205, -3.869898855143417, -18.01518487110813, -17.38504309777226, -29.7102253995114, -33.97262688823771, -25.58952900757811, -18.32327569996284, -10.43679078115309, -17.34797699860558, -23.44071853477707, -20.13369389964067, -16.23209205498968, -20.84681207056716, -13.14211233137375, -11.68410006052765, -15.49850331840433, -12.80349920668154, -9.951696917262908, -9.674794006047554, -13.35878598779897, -23.86875827725563, -13.92120845548608, -15.25915378398707, -14.40626012443236, -21.26593666732801, -15.47805189201786, -20.8967440084538, -17.92205772755303, -21.52612599164656, -14.37849206841925, -11.28236683284286, -27.85944578501297, -7.045007615754844, -35.50167243235479, -15.43207104477209, -4.330649700739783, -4.821509537453836, -24.61117309405466, -19.66210749973598, -19.61978108110112, -13.06931658869425, -18.90379736902437, -15.17248506099829, -24.20575482256608, -16.80670782290678, -15.1069403318206, -20.23445804273289, -22.93238636351499, -28.6422792678352, -31.91671871385733, -19.7070935797896, -24.16184701754757, -32.87373578813684, -25.97502236883938, -30.04305670719911, -20.66008132977401, -22.5476319199698, -15.71574496122768, -21.82260087605331, -22.33213004101708, -17.88649192977146, -22.85979453942399, -13.9142190617628, -10.20989813642594, -19.67318749886311, -13.22545647691756, -11.35738362057711, -10.37800058317319, -9.86308947602663, -20.98168478524144, -5.038213419512004, -12.8612703045419, -23.7103757747438, -25.78805046306136, -29.5117411496098, -15.02489637507387, -32.51478386333478, -15.48689562410333, -23.58179278538965, -10.7011656905293, -12.18338021676437, -11.80719456318334, -34.37559964635795, -21.96698531834351, -15.96606915985646, -18.18645503653203, -23.73685168133605, -15.7426553469114, -11.56446818066272, -21.42813665189797, -23.10666793730778, -24.26053675245742, -14.08444644301535, -23.12886976791419, -13.54997092114479, -24.18202649171034, -13.43311848775762, -18.68125871223531, -14.34963037446899, -21.30807004664649, -11.23675042114956, -20.25521737033718, -11.41928014036639, -23.0616314567799, -12.74836397165115, -8.946938971416877, -21.33592841357732, -18.29022453494306, -23.78096262851221, -10.26615870794974, -23.87195921412485, -7.045007615754844, -27.36975377176551, -13.02213773679562, -24.88461586299227, -9.937370797941819, -20.9215542254461, -13.7430158107626, -13.32781861737069, -16.57378722435969, -13.1562876406111, -18.65461183747465, -12.88434508060274, -25.53251613794421, -23.47076517726, -12.38103504563448, -18.08858152438308, -13.3986078002421, -24.83005553415067, -13.48186232123563, -12.76305322156708, -14.99349220446663, -12.68915386346622, -15.16813193431097, -20.38979714624436, -17.1398617656887, -21.99353054090562, -31.80290581785966, -34.17165493312128, -28.14103833717329, -23.01519425280903, -25.32718282655863, -24.9256764033518, -27.36738567584731, -23.63994953138027, -12.19474154438638, -21.8509764153975, -14.27265880961605, -27.81140090827595, -16.66595175805092, -15.90073698436111, -16.04898816099204, -16.77891193093655, -15.05041271240863, -18.6937096770671, -20.92753847593657, -26.68202074910777, -22.68645320525759, -30.02139727511975, -14.61774067439237, -10.02271219166692, -14.02556111130297, -22.35631047609814, -17.23179491687371, -27.80786897153735, -7.71222261637312, -29.01667081229076, -12.42383366521858, -14.96109424540947, -20.51828142366711, -13.95474218677742, -25.26930987352585, -25.30942633816443, -29.95264501627203, -17.87797633090322, -29.28864522431501, -18.28270560387423, -26.07314333903045, -9.265582530948477, -19.57038320696334, -13.84155482021799, -13.76410195180156, -10.09880900833976, -10.13770828948875, -20.68018631936204]
+    ]
+  },
+ "Evidence Ratios":{
+   "constrained":[
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+    ],
+   "optimized null":[
+    [1.249959400407102, 0.9958881520275259, 0.998207509265751, 1.022475766760606, 0.7329779279148643, 0.7355512219978014, 3.215747411518881, 3.831944066897763, 2.992504567232528, 0.8236645230667027, 0.8159500030737468, 1.396476901447714, 0.9750384449114691, 1.16417536866286, 0.2928545373193804, 0.8738264187311083, 1.116680407100678, 1.610657107893188, 1.633098870338358, 1.076295106848796, 1.478341111181925, 1.708669953055735, 0.6501772588199817, 0.8228834033449909, 1.578122886012883, 1.176644073870286, 1.028238233000157, 1.311743164559289, 0.8005936991596435, 0.4612384787800625, 0.4054241751261601, 0.7141843613652971, 1.380541560105011, 0.6731713608501634, 0.932626077339456, 1.376173789613603, 0.6010146384105997, 1.000648214046449, 1.010762802431324, 1.279765846941387, 0.8252095291075795, 0.5488172901332377, 2.905327825256244, 0.4694117092940189, 0.952073347603641, 0.9820568432858974, 0.9684541283622321, 0.7465802831481059, 0.725817575723242, 0.6897980335692911, 0.4519945356959116, 1.644970489890064, 0.6861498379435136, 11.73909248217663, 4.87996237464428, 0.8976824471171899, 2.965984233784409, 0.733133747843722, 0.7183950548657764, 0.6781158778869135, 1.202933169206003, 1.041670940984456, 0.6239400537888191, 0.864005597730941, 0.8863622283336499, 2.211207115702391, 2.415912028974954, 1.558641206543682, 1.178733082401182, 1.144859074170125, 1.052449670353621, 0.9907345967710618, 0.9999999999999973, 1.635182470378155, 0.9532802729006801, 4.075002787751862, 0.7547233152543775, 0.9913306590671749, 10.61305441401069, 1.087472394658304, 2.031666990662131, 0.8935759463782673, 0.7504804700650514, 1.07138642619565, 0.7779921221867564, 0.3692230071631759, 0.5095967222916621, 0.852637781481885, 0.492890538993211, 1.010746910759831, 2.039528413292879, 1.943271153632765, 1.264662551213628, 1.075020419076957, 1.352742324566819, 1.108889296748787, 0.9128213876445376, 1.605270076656883, 0.9963188974862515, 1.369641261789208, 1.110930409345364, 1.759465308015671, 1.041233006895448, 0.7072388659882123, 1.020994825899436, 0.7775662346759626, 1.396238093640341, 1.417000739126258, 1.223497018037751, 0.6592994704264704, 0.7683951448151665, 1.315289046185217, 2.744051160985256, 0.932626077339456, 0.8295939599329692, 1.161718436561281, 1.485979405967741, 1.157190740711233, 0.5180077437805523, 1.005418861153479, 1.872838124227439, 1.909650007781456, 0.9095327119137432, 0.4044301708455042, 1.105326473224138, 1.202728682967098, 1.287402785135559, 1.665642405761295, 0.7767263119192113, 1.006545375541812, 4.958869792471186, 0.8264897380438972, 1.126750821714303, 0.7872722189265667, 1.249979829536444, 0.5392540993266187, 0.900764623315236, 1.480325818230283, 1.853802344884983, 0.8908173136045756, 3.516872648338504, 1.028849304595149, 0.7637780328545294, 1.275961818909257, 1.7479680529214, 0.6149407328711725, 2.288611307253957, 1.143103773111974, 1.134112880938005, 0.6144610028110447, 3.50665225694476, 1.967609019313462, 0.4619393418252924, 1.170835076724906, 0.713460509830789, 0.907767204501339, 0.5897350692995594, 2.180804513956808, 0.6191414671741319, 0.8918751295230388, 1.472219881303941, 0.7738252314079443, 0.9349092081542767, 0.9591890032827355, 2.234571675884028, 0.5165519486568414, 2.268523145559755, 1.592316727559848, 0.9190552183615908, 1.63878552010542, 1.726996028513171, 1.33659173528842, 1.007491351842102, 2.384818706326968, 2.080787852232155, 2.049282389773126, 0.6134033430403113, 1.067413275400906, 1.720346037637947, 0.6260135038640929, 1.365837060781729, 0.4917881296168616, 0.7773205034026993, 0.7635232604405103, 1.969025623887814, 1.950874776061578, 1.759983366341118]
+    ]
+  },
+ "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"
+    }
+  },
+ "data partitions":{
+   "0":{
+     "name":"busted.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,
+       "MG94xREV with separate rates for branch sets":0,
+       "unconstrained":0,
+       "constrained":0
+      },
+     "Chimp":{
+       "original name":"Chimp",
+       "Nucleotide GTR":0.001818647577470898,
+       "MG94xREV with separate rates for branch sets":0.001828142895085465,
+       "unconstrained":0.001835079043904073,
+       "constrained":0.001827227299324197
+      },
+     "Baboon":{
+       "original name":"Baboon",
+       "Nucleotide GTR":0.001683434956773037,
+       "MG94xREV with separate rates for branch sets":0.001771624553208579,
+       "unconstrained":0.001852571561323465,
+       "constrained":0.001757260248005238
+      },
+     "RhMonkey":{
+       "original name":"RhMonkey",
+       "Nucleotide GTR":0.003773669075849421,
+       "MG94xREV with separate rates for branch sets":0.003717699096857038,
+       "unconstrained":0.003672835047422234,
+       "constrained":0.00373144096412681
+      },
+     "Cow":{
+       "original name":"Cow",
+       "Nucleotide GTR":0.2483322373763571,
+       "MG94xREV with separate rates for branch sets":0.2480141631033857,
+       "unconstrained":0.2960120156157274,
+       "constrained":0.2592686681333873
+      },
+     "Pig":{
+       "original name":"Pig",
+       "Nucleotide GTR":0.187244836750842,
+       "MG94xREV with separate rates for branch sets":0.1926081878751187,
+       "unconstrained":0.2187526946336905,
+       "constrained":0.1943776301130502
+      },
+     "Horse":{
+       "original name":"Horse",
+       "Nucleotide GTR":0.2091766851769093,
+       "MG94xREV with separate rates for branch sets":0.2111575880588217,
+       "unconstrained":0.2572135566477119,
+       "constrained":0.218486450878766
+      },
+     "Cat":{
+       "original name":"Cat",
+       "Nucleotide GTR":0.266381043956941,
+       "MG94xREV with separate rates for branch sets":0.273601177885004,
+       "unconstrained":0.3292215104251173,
+       "constrained":0.28483085314287
+      },
+     "Mouse":{
+       "original name":"Mouse",
+       "Nucleotide GTR":0.1181831744338598,
+       "MG94xREV with separate rates for branch sets":0.1201847378516324,
+       "unconstrained":0.1489713993010398,
+       "constrained":0.1233480139851019
+      },
+     "Rat":{
+       "original name":"Rat",
+       "Nucleotide GTR":0.06669700444436912,
+       "MG94xREV with separate rates for branch sets":0.0670850471739789,
+       "unconstrained":0.07366345007817726,
+       "constrained":0.06713082546371778
+      },
+     "Node1":{
+       "Nucleotide GTR":0.276880831396131,
+       "MG94xREV with separate rates for branch sets":0.2843521449765504,
+       "unconstrained":0.459085769955035,
+       "constrained":0.3115534692518958
+      },
+     "Node12":{
+       "Nucleotide GTR":0.01783434870161725,
+       "MG94xREV with separate rates for branch sets":0.01788794906051452,
+       "unconstrained":0.01828498503175797,
+       "constrained":0.01770410398930177
+      },
+     "Node2":{
+       "Nucleotide GTR":0.06617535490721377,
+       "MG94xREV with separate rates for branch sets":0.06447679597474805,
+       "unconstrained":0.0623969317369398,
+       "constrained":0.06097949807503514
+      },
+     "Node3":{
+       "Nucleotide GTR":0.09884524766349881,
+       "MG94xREV with separate rates for branch sets":0.1017497956116402,
+       "unconstrained":0.1285021744856729,
+       "constrained":0.1065011238088613
+      },
+     "Node8":{
+       "Nucleotide GTR":0.1061610073141143,
+       "MG94xREV with separate rates for branch sets":0.1093806684969149,
+       "unconstrained":0.1348034716617685,
+       "constrained":0.1118205234697939
+      },
+     "Node9":{
+       "Nucleotide GTR":0.02568007351415409,
+       "MG94xREV with separate rates for branch sets":0.02593963430985144,
+       "unconstrained":0.02761127562964508,
+       "constrained":0.02639493109700932
+      }
+    },
+   "attributes":{
+     "original name":{
+       "attribute type":"node label",
+       "display order":0
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "MG94xREV with separate rates for branch sets":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "unconstrained":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "constrained":{
+       "attribute type":"branch length",
+       "display order":1
+      }
+    }
+  },
+ "test results":{
+   "LRT":44.77492170961614,
+   "p-value":1.893429857346973e-10
+  }
+}
\ No newline at end of file