diff test-data/absrel-out1.json @ 35:841557158611 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

--- a/test-data/absrel-out1.json	Thu Aug 18 14:05:48 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,478 +0,0 @@
-{
- "analysis":{
-   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
-   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",
-   "contact":"[e-mail]",
-   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
-   "requirements":"in-frame codon alignment and a phylogenetic tree",
-   "version":"2.2"
-  },
- "branch attributes":{
-   "0":{
-     "Baboon":{
-       "Baseline MG94xREV":0.001816807585564731,
-       "Baseline MG94xREV omega ratio":0,
-       "Corrected P-value":1,
-       "Full adaptive model":0.001810407118394509,
-       "LRT":0,
-       "Nucleotide GTR":0.001678881906620672,
-       "Rate Distributions":        [
-[0, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "original name":"Baboon",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Cat":{
-       "Baseline MG94xREV":0.2286001363527903,
-       "Baseline MG94xREV omega ratio":1.403298474422089,
-       "Corrected P-value":1,
-       "Full adaptive model":0.1219386838393392,
-       "LRT":1.644967676056694,
-       "Nucleotide GTR":0.265904547400163,
-       "Rate Distributions":        [
-[0.2130519766306851, 0.6352283641519592],
-        [2.628217450705319, 0.3647716358480408] 
-        ],
-       "Rate classes":2,
-       "Uncorrected P-value":0.171730764045231,
-       "original name":"Cat",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Chimp":{
-       "Baseline MG94xREV":0.001840311209746262,
-       "Baseline MG94xREV omega ratio":10000000000,
-       "Corrected P-value":1,
-       "Full adaptive model":0.001841979303044237,
-       "LRT":0.6159123786974305,
-       "Nucleotide GTR":0.001816713800925801,
-       "Rate Distributions":        [
-[10000000000, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":0.3069983227523322,
-       "original name":"Chimp",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Cow":{
-       "Baseline MG94xREV":0.2070244948790512,
-       "Baseline MG94xREV omega ratio":2.153434974462683,
-       "Corrected P-value":0.5006146299996015,
-       "Full adaptive model":0.1241125417707662,
-       "LRT":4.898194538953248,
-       "Nucleotide GTR":0.2481512612523618,
-       "Rate Distributions":        [
-[0, 0.52318726440949],
-        [2.444056517734385, 0.47681273559051] 
-        ],
-       "Rate classes":2,
-       "Uncorrected P-value":0.03128841437497509,
-       "original name":"Cow",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Horse":{
-       "Baseline MG94xREV":0.190365915457708,
-       "Baseline MG94xREV omega ratio":1.182933895494305,
-       "Corrected P-value":1,
-       "Full adaptive model":0.0869489794025302,
-       "LRT":2.047309801283518,
-       "Nucleotide GTR":0.2090927256979082,
-       "Rate Distributions":        [
-[0, 0.5397658078247131],
-        [1.633257246666139, 0.4602341921752869] 
-        ],
-       "Rate classes":2,
-       "Uncorrected P-value":0.1382789032066179,
-       "original name":"Horse",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Human":{
-       "Baseline MG94xREV":0,
-       "Baseline MG94xREV omega ratio":1,
-       "Corrected P-value":1,
-       "Full adaptive model":0,
-       "LRT":0,
-       "Nucleotide GTR":0,
-       "Rate Distributions":        [
-[1, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "original name":"Human",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574
-      },
-     "Mouse":{
-       "Baseline MG94xREV":0.1083167307250788,
-       "Baseline MG94xREV omega ratio":0.5108576904540283,
-       "Corrected P-value":1,
-       "Full adaptive model":0.1078010043714489,
-       "LRT":0,
-       "Nucleotide GTR":0.1181001275359051,
-       "Rate Distributions":        [
-[0.5087375113796073, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "original name":"Mouse",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548
-      },
-     "Node1":{
-       "Baseline MG94xREV":0.2542393300501047,
-       "Baseline MG94xREV omega ratio":0.2997498382776075,
-       "Corrected P-value":1,
-       "Full adaptive model":0.2550466752020236,
-       "LRT":0,
-       "Nucleotide GTR":0.2767426965701868,
-       "Rate Distributions":        [
-[0.2932817609633239, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921
-      },
-     "Node12":{
-       "Baseline MG94xREV":0.01400815185374474,
-       "Baseline MG94xREV omega ratio":0.2754467062829232,
-       "Corrected P-value":1,
-       "Full adaptive model":0.01437973904273591,
-       "LRT":0,
-       "Nucleotide GTR":0.01784721909304638,
-       "Rate Distributions":        [
-[0.3037614070859027, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814
-      },
-     "Node2":{
-       "Baseline MG94xREV":0.0400106272595141,
-       "Baseline MG94xREV omega ratio":0.116408812566168,
-       "Corrected P-value":1,
-       "Full adaptive model":0.03991940069030483,
-       "LRT":0,
-       "Nucleotide GTR":0.06613304839358287,
-       "Rate Distributions":        [
-[0.1193993042178124, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122
-      },
-     "Node3":{
-       "Baseline MG94xREV":0.08548068002443369,
-       "Baseline MG94xREV omega ratio":1.293385437932658,
-       "Corrected P-value":1,
-       "Full adaptive model":0.08590119038008139,
-       "LRT":0.1383887036890883,
-       "Nucleotide GTR":0.09881178513658169,
-       "Rate Distributions":        [
-[1.330576641567385, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":0.4219212196398351,
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498
-      },
-     "Node8":{
-       "Baseline MG94xREV":0.09463393920061362,
-       "Baseline MG94xREV omega ratio":1.862136443854597,
-       "Corrected P-value":1,
-       "Full adaptive model":0.0958035263641453,
-       "LRT":0.7150293976401372,
-       "Nucleotide GTR":0.1062333225692588,
-       "Rate Distributions":        [
-[1.883870769808856, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":0.2893795680778183,
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092
-      },
-     "Node9":{
-       "Baseline MG94xREV":0.02846111726225027,
-       "Baseline MG94xREV omega ratio":0.4321055128385307,
-       "Corrected P-value":1,
-       "Full adaptive model":0.02810856974543091,
-       "LRT":0,
-       "Nucleotide GTR":0.02566185438854229,
-       "Rate Distributions":        [
-[0.4185836885800617, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      },
-     "Pig":{
-       "Baseline MG94xREV":0.1782835053555321,
-       "Baseline MG94xREV omega ratio":1.275728452678247,
-       "Corrected P-value":1,
-       "Full adaptive model":0.1729188354138871,
-       "LRT":0.3324036585026988,
-       "Nucleotide GTR":0.1871760137183495,
-       "Rate Distributions":        [
-[1.235108129487059, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":0.3669120164240152,
-       "original name":"Pig",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695
-      },
-     "Rat":{
-       "Baseline MG94xREV":0.06315403896300904,
-       "Baseline MG94xREV omega ratio":0.8744850915248316,
-       "Corrected P-value":1,
-       "Full adaptive model":0.06408078523886611,
-       "LRT":0,
-       "Nucleotide GTR":0.0666364425850592,
-       "Rate Distributions":        [
-[0.8782045320352186, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":1,
-       "original name":"Rat",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0.1346164190615118
-      },
-     "RhMonkey":{
-       "Baseline MG94xREV":0.003671939837747083,
-       "Baseline MG94xREV omega ratio":10000000000,
-       "Corrected P-value":1,
-       "Full adaptive model":0.003675047654636179,
-       "LRT":1.165062770327495,
-       "Nucleotide GTR":0.003777016173741061,
-       "Rate Distributions":        [
-[10000000000, 1] 
-        ],
-       "Rate classes":1,
-       "Uncorrected P-value":0.2236284592802686,
-       "original name":"RhMonkey",
-       "rate at which 2 nucleotides are changed instantly within a single codon":0
-      }
-    },
-   "attributes":{
-     "Baseline MG94xREV":{
-       "attribute type":"branch length",
-       "display order":1
-      },
-     "Baseline MG94xREV omega ratio":{
-       "attribute type":"branch label",
-       "display order":1
-      },
-     "Corrected P-value":{
-       "attribute type":"branch label",
-       "display order":6
-      },
-     "Full adaptive model":{
-       "attribute type":"branch length",
-       "display order":2
-      },
-     "LRT":{
-       "attribute type":"branch label",
-       "display order":4
-      },
-     "Nucleotide GTR":{
-       "attribute type":"branch length",
-       "display order":0
-      },
-     "Rate Distributions":{
-       "attribute type":"branch label",
-       "display order":3
-      },
-     "Rate classes":{
-       "attribute type":"branch label",
-       "display order":2
-      },
-     "Uncorrected P-value":{
-       "attribute type":"branch label",
-       "display order":5
-      },
-     "original name":{
-       "attribute type":"node label",
-       "display order":-1
-      },
-     "rate at which 2 nucleotides are changed instantly within a single codon":{
-       "attribute type":"branch label",
-       "display order":7
-      }
-    }
-  },
- "data partitions":{
-   "0":{
-     "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] 
-      ],
-     "name":"absrel.filter.default"
-    }
-  },
- "fits":{
-   "Baseline MG94xREV":{
-     "AIC-c":6983.763305606333,
-     "Equilibrium frequencies":      [
-[0.04875339327772683],
-      [0.03982858547830345],
-      [0.04946803524790992],
-      [0.04152216138298744],
-      [0.01811683453600613],
-      [0.01480036248560469],
-      [0.0183823965708893],
-      [0.01542969784826435],
-      [0.01894694796506697],
-      [0.01547851515238824],
-      [0.01922467805342367],
-      [0.01613668666381816],
-      [0.02832099415740372],
-      [0.02313654621336914],
-      [0.02873613184734657],
-      [0.02412034959764736],
-      [0.01662182431200483],
-      [0.01357902918971745],
-      [0.01686547203528639],
-      [0.01415643148428886],
-      [0.006176695005242439],
-      [0.005045987744654046],
-      [0.006267234867003878],
-      [0.005260551308914496],
-      [0.006459711194459957],
-      [0.005277194922783805],
-      [0.006554399593040238],
-      [0.005501589790395056],
-      [0.009655668202293983],
-      [0.007888099278638223],
-      [0.009797203904398108],
-      [0.008223514024394991],
-      [0.03326722643528176],
-      [0.02717732003095303],
-      [0.03375486749252685],
-      [0.02833294365668738],
-      [0.01236215156074466],
-      [0.01009913314808799],
-      [0.01254335971371867],
-      [0.01052856463184265],
-      [0.01292858539344675],
-      [0.0105618754683007],
-      [0.0131180965046964],
-      [0.01101098350431497],
-      [0.0193250328267319],
-      [0.01578738770911659],
-      [0.0196083049972345],
-      [0.01645869298147252],
-      [0.01962343746171723],
-      [0.02045785777700414],
-      [0.008926115885166477],
-      [0.007292098982657142],
-      [0.009056957588961733],
-      [0.007602170831388156],
-      [0.007626222986467745],
-      [0.009471947420992787],
-      [0.007950502328516303],
-      [0.01395367801862353],
-      [0.01139931439306339],
-      [0.01415821524731906],
-      [0.01188403168729233] 
-      ],
-     "Log Likelihood":-3427.720059001285,
-     "Rate Distributions":{
-       "Per-branch delta":{
-         "2.5%":0,
-         "97.5%":12.07373117808175,
-         "Mean":1.277646334033236,
-         "Median":0.4551223038316586
-        },
-       "Per-branch omega":{
-         "2.5%":0,
-         "97.5%":2.153434974462683,
-         "Mean":666666667.5119981,
-         "Median":1
-        }
-      },
-     "display order":1,
-     "estimated parameters":62
-    },
-   "Full adaptive model":{
-     "AIC-c":6972.859938351839,
-     "Log Likelihood":-3415.824749853321,
-     "Rate Distributions":{
-      },
-     "display order":2,
-     "estimated parameters":68
-    },
-   "Nucleotide GTR":{
-     "AIC-c":7112.857317645923,
-     "Equilibrium frequencies":      [
-[0.3592490842490842],
-      [0.181959706959707],
-      [0.240018315018315],
-      [0.2187728937728937] 
-      ],
-     "Log Likelihood":-3532.321228205235,
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,
-       "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,
-       "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,
-       "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399
-      },
-     "display order":0,
-     "estimated parameters":24
-    }
-  },
- "input":{
-   "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",
-   "number of sequences":10,
-   "number of sites":187,
-   "partition count":1,
-   "trees":{
-     "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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)"
-    }
-  },
- "test results":{
-   "P-value threshold":0.05,
-   "positive test results":0,
-   "tested":16
-  },
- "tested":{
-   "0":{
-     "Baboon":"test",
-     "Cat":"test",
-     "Chimp":"test",
-     "Cow":"test",
-     "Horse":"test",
-     "Human":"test",
-     "Mouse":"test",
-     "Node1":"test",
-     "Node12":"test",
-     "Node2":"test",
-     "Node3":"test",
-     "Node8":"test",
-     "Node9":"test",
-     "Pig":"test",
-     "Rat":"test",
-     "RhMonkey":"test"
-    }
-  },
- "timers":{
-   "Baseline model fitting":{
-     "order":2,
-     "timer":17
-    },
-   "Complexity analysis":{
-     "order":3,
-     "timer":110
-    },
-   "Full adaptive model fitting":{
-     "order":4,
-     "timer":20
-    },
-   "Overall":{
-     "order":0,
-     "timer":259
-    },
-   "Preliminary model fitting":{
-     "order":1,
-     "timer":0
-    },
-   "Testing for selection":{
-     "order":5,
-     "timer":112
-    }
-  }
-}
\ No newline at end of file