diff test-data/busted-out1.json @ 35:ec783806a5c3 draft default tip

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

--- a/test-data/busted-out1.json	Thu Aug 18 13:53:29 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,394 +0,0 @@
-{
- "Evidence Ratios":{
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-  ],
- "analysis":{
-   "authors":"Sergei L Kosakovsky Pond",
-   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
-   "contact":"[e-mail]",
-   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
-   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
-   "version":"3.1"
-  },
- "background":0,
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-       "Nucleotide GTR":0.001680040630127455,
-       "constrained":0.001513413708231178,
-       "original name":"Baboon",
-       "unconstrained":0.00161713005248515
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-       "Nucleotide GTR":0.2660909938917123,
-       "constrained":0.3466844629529476,
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-      },
-     "Chimp":{
-       "MG94xREV with separate rates for branch sets":0.001828401123834132,
-       "Nucleotide GTR":0.001818373670119325,
-       "constrained":0.001854421055569225,
-       "original name":"Chimp",
-       "unconstrained":0.001853794709397617
-      },
-     "Cow":{
-       "MG94xREV with separate rates for branch sets":0.2477981038577003,
-       "Nucleotide GTR":0.2481025999892287,
-       "constrained":0.3115800338446564,
-       "original name":"Cow",
-       "unconstrained":0.3266266518611717
-      },
-     "Horse":{
-       "MG94xREV with separate rates for branch sets":0.21116782461044,
-       "Nucleotide GTR":0.2090310577070883,
-       "constrained":0.2473423214593362,
-       "original name":"Horse",
-       "unconstrained":0.2568895651944081
-      },
-     "Human":{
-       "MG94xREV with separate rates for branch sets":0,
-       "Nucleotide GTR":0,
-       "constrained":0,
-       "original name":"Human",
-       "unconstrained":0
-      },
-     "Mouse":{
-       "MG94xREV with separate rates for branch sets":0.1200804161847832,
-       "Nucleotide GTR":0.1180171198334285,
-       "constrained":0.1381882260320684,
-       "original name":"Mouse",
-       "unconstrained":0.1482500840848965
-      },
-     "Node1":{
-       "MG94xREV with separate rates for branch sets":0.2841417945012228,
-       "Nucleotide GTR":0.2767237570684924,
-       "constrained":0.3893703941610758,
-       "unconstrained":0.4535373691584812
-      },
-     "Node12":{
-       "MG94xREV with separate rates for branch sets":0.01789005959388253,
-       "Nucleotide GTR":0.01784803874223016,
-       "constrained":0.01603697675468384,
-       "unconstrained":0.01716581823757766
-      },
-     "Node2":{
-       "MG94xREV with separate rates for branch sets":0.06425321743363792,
-       "Nucleotide GTR":0.06613162123865737,
-       "constrained":0.06766882319669908,
-       "unconstrained":0.06748821329187271
-      },
-     "Node3":{
-       "MG94xREV with separate rates for branch sets":0.1017634409613201,
-       "Nucleotide GTR":0.09886326330774685,
-       "constrained":0.128627313187861,
-       "unconstrained":0.1385358286963005
-      },
-     "Node8":{
-       "MG94xREV with separate rates for branch sets":0.1095532710088725,
-       "Nucleotide GTR":0.106239268140425,
-       "constrained":0.1326559254556453,
-       "unconstrained":0.1430782720540034
-      },
-     "Node9":{
-       "MG94xREV with separate rates for branch sets":0.02590764371262369,
-       "Nucleotide GTR":0.02566573875750134,
-       "constrained":0.02991066003065707,
-       "unconstrained":0.02952913741456189
-      },
-     "Pig":{
-       "MG94xREV with separate rates for branch sets":0.1925158663261413,
-       "Nucleotide GTR":0.1871893456388788,
-       "constrained":0.2351007649069627,
-       "original name":"Pig",
-       "unconstrained":0.248176820169511
-      },
-     "Rat":{
-       "MG94xREV with separate rates for branch sets":0.06699144002108472,
-       "Nucleotide GTR":0.06661283005976348,
-       "constrained":0.06832918896283274,
-       "original name":"Rat",
-       "unconstrained":0.07114161288708017
-      },
-     "RhMonkey":{
-       "MG94xREV with separate rates for branch sets":0.003716234330029482,
-       "Nucleotide GTR":0.003775170135617877,
-       "constrained":0.004078975866589158,
-       "original name":"RhMonkey",
-       "unconstrained":0.003977618821878279
-      }
-    },
-   "attributes":{
-     "MG94xREV with separate rates for branch sets":{
-       "attribute type":"branch length",
-       "display order":1
-      },
-     "Nucleotide GTR":{
-       "attribute type":"branch length",
-       "display order":0
-      },
-     "constrained":{
-       "attribute type":"branch length",
-       "display order":1
-      },
-     "original name":{
-       "attribute type":"node label",
-       "display order":0
-      },
-     "unconstrained":{
-       "attribute type":"branch length",
-       "display order":0
-      }
-    }
-  },
- "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":"busted.filter.default"
-    }
-  },
- "fits":{
-   "Constrained model":{
-     "AIC-c":6918.865252134614,
-     "Log Likelihood":-3419.580167050914,
-     "Rate Distributions":{
-       "Synonymous site-to-site rates":{
-         "0":{
-           "proportion":0.3286044813984554,
-           "rate":0.3114745230555425
-          },
-         "1":{
-           "proportion":0.5759073485616787,
-           "rate":1.038727366194607
-          },
-         "2":{
-           "proportion":0.09548817003986594,
-           "rate":3.135858111155513
-          }
-        },
-       "Test":{
-         "0":{
-           "omega":0,
-           "proportion":0.1610337459523823
-          },
-         "1":{
-           "omega":0.9239856235614761,
-           "proportion":0
-          },
-         "2":{
-           "omega":1,
-           "proportion":0.8389662540476177
-          }
-        }
-      },
-     "display order":3,
-     "estimated parameters":39
-    },
-   "MG94xREV with separate rates for branch sets":{
-     "AIC-c":6997.104847699299,
-     "Equilibrium frequencies":      [
-[0.04876086397632926],
-      [0.03982224127745371],
-      [0.0494959405650269],
-      [0.04152830682371345],
-      [0.01810345074594235],
-      [0.01478480742075003],
-      [0.01837636270304883],
-      [0.01541821854326533],
-      [0.01892910005547028],
-      [0.01545910240515689],
-      [0.01921445878706794],
-      [0.01612140169177368],
-      [0.02829747763884322],
-      [0.02311011106415996],
-      [0.02872406592369408],
-      [0.02410019507229243],
-      [0.01663805943190806],
-      [0.01358804506433061],
-      [0.01688888041768248],
-      [0.01417018446135155],
-      [0.006177213955434187],
-      [0.005044834822351987],
-      [0.006270336287397383],
-      [0.00526096577332031],
-      [0.006458939937330408],
-      [0.005274916061901906],
-      [0.006556309326397028],
-      [0.005500904159606446],
-      [0.009655594186286731],
-      [0.007885574003572761],
-      [0.009801153568494354],
-      [0.008223407979974132],
-      [0.03327785448210915],
-      [0.02717750758119989],
-      [0.03377952261833742],
-      [0.02834184710178207],
-      [0.01235507229404208],
-      [0.01009019590244688],
-      [0.01254132667213156],
-      [0.01052248035033209],
-      [0.01291855364640413],
-      [0.01055038238273567],
-      [0.01311330258173711],
-      [0.01100238215235291],
-      [0.01931219560697892],
-      [0.0157719705998612],
-      [0.01960332955558842],
-      [0.01644767379420349],
-      [0.01965132601881859],
-      [0.02049322866376102],
-      [0.008933621043463411],
-      [0.007295949736387736],
-      [0.009068296583349953],
-      [0.007608523013862737],
-      [0.007628698224327205],
-      [0.009481877006094248],
-      [0.00795552712159237],
-      [0.01396413011303752],
-      [0.01140428846505027],
-      [0.01417464125436193],
-      [0.01189287130232129] 
-      ],
-     "Log Likelihood":-3467.012706765863,
-     "Rate Distributions":{
-       "non-synonymous/synonymous rate ratio for *test*":        [
-[0.9959842858928788, 1] 
-        ]
-      },
-     "display order":1,
-     "estimated parameters":31
-    },
-   "Nucleotide GTR":{
-     "AIC-c":7112.857310169033,
-     "Equilibrium frequencies":      [
-[0.3592490842490842],
-      [0.181959706959707],
-      [0.240018315018315],
-      [0.2187728937728937] 
-      ],
-     "Log Likelihood":-3532.32122446679,
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
-       "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
-       "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
-       "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
-      },
-     "display order":0,
-     "estimated parameters":24
-    },
-   "Unconstrained model":{
-     "AIC-c":6910.776988890891,
-     "Log Likelihood":-3414.491829601268,
-     "Rate Distributions":{
-       "Synonymous site-to-site rates":{
-         "0":{
-           "proportion":0.2655037162058198,
-           "rate":0.2749303122566129
-          },
-         "1":{
-           "proportion":0.6321791898264187,
-           "rate":0.9740711294478059
-          },
-         "2":{
-           "proportion":0.1023170939677615,
-           "rate":3.041695877803997
-          }
-        },
-       "Test":{
-         "0":{
-           "omega":0,
-           "proportion":0.386646389823596
-          },
-         "1":{
-           "omega":0.9964438830494696,
-           "proportion":0
-          },
-         "2":{
-           "omega":1.876622752045829,
-           "proportion":0.613353610176404
-          }
-        }
-      },
-     "display order":2,
-     "estimated parameters":40
-    }
-  },
- "input":{
-   "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",
-   "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":{
-   "LRT":10.17667489929045,
-   "p-value":0.003084133210483175
-  },
- "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":{
-   "Constrained BUSTED model fitting":{
-     "order":3,
-     "timer":70
-    },
-   "Overall":{
-     "order":0,
-     "timer":451
-    },
-   "Preliminary model fitting":{
-     "order":1,
-     "timer":10
-    },
-   "Unconstrained BUSTED model fitting":{
-     "order":2,
-     "timer":370
-    }
-  }
-}
\ No newline at end of file