diff test-data/relax-out1.json @ 33:5b6b8b08f1a9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"

--- a/test-data/relax-out1.json	Sat Nov 27 11:28:17 2021 +0000
+++ b/test-data/relax-out1.json	Wed Mar 30 00:17:25 2022 +0000
@@ -3,53 +3,53 @@
  "branch attributes":{
    "0":{
      "Baboon":{
-       "General descriptive":0.001858767762813579,
-       "MG94xREV with separate rates for branch sets":0.001769472024099301,
-       "Nucleotide GTR":0.001680040630127455,
-       "RELAX alternative":0.001872256662230973,
-       "RELAX null":0.001855569334462731,
-       "RELAX partitioned descriptive":0.001898170574782418,
-       "k (general descriptive)":0.09971581394819819,
+       "General descriptive":0.001859058366368826,
+       "MG94xREV with separate rates for branch sets":0.001769294089885709,
+       "Nucleotide GTR":0.001685167654714891,
+       "RELAX alternative":0.001873708670384941,
+       "RELAX null":0.001859167714920677,
+       "RELAX partitioned descriptive":0.001898817195216417,
+       "k (general descriptive)":0.09969742933359635,
        "original name":"Baboon"
       },
      "Cat":{
-       "General descriptive":0.3644803308678196,
-       "MG94xREV with separate rates for branch sets":0.2796030091674721,
-       "Nucleotide GTR":0.2660909938917123,
-       "RELAX alternative":0.3689219388980864,
-       "RELAX null":0.3256077554105627,
-       "RELAX partitioned descriptive":0.3717219559832593,
-       "k (general descriptive)":2.314507643873676,
+       "General descriptive":0.3650161006190072,
+       "MG94xREV with separate rates for branch sets":0.2796018473093496,
+       "Nucleotide GTR":0.2660536011315811,
+       "RELAX alternative":0.3685874431614762,
+       "RELAX null":0.3167334440346762,
+       "RELAX partitioned descriptive":0.3719472357609613,
+       "k (general descriptive)":2.319877215422834,
        "original name":"Cat"
       },
      "Chimp":{
-       "General descriptive":0.001848680051431209,
-       "MG94xREV with separate rates for branch sets":0.001825434296531533,
-       "Nucleotide GTR":0.001818373670119325,
-       "RELAX alternative":0.001831703934281931,
-       "RELAX null":0.00183525802483954,
-       "RELAX partitioned descriptive":0.001832717232153088,
-       "k (general descriptive)":5.261186652622472,
+       "General descriptive":0.001895983937468787,
+       "MG94xREV with separate rates for branch sets":0.001826027667597702,
+       "Nucleotide GTR":0.001820258053351119,
+       "RELAX alternative":0.001831530791728368,
+       "RELAX null":0.001834052740714585,
+       "RELAX partitioned descriptive":0.001832682515795942,
+       "k (general descriptive)":5.158328270628251,
        "original name":"Chimp"
       },
      "Cow":{
-       "General descriptive":0.3733627618450006,
-       "MG94xREV with separate rates for branch sets":0.2520490246808783,
-       "Nucleotide GTR":0.2481025999892287,
-       "RELAX alternative":0.342739998512865,
-       "RELAX null":0.2948256709356563,
-       "RELAX partitioned descriptive":0.3466331923230422,
-       "k (general descriptive)":2.846155982935764,
+       "General descriptive":0.3737128696500712,
+       "MG94xREV with separate rates for branch sets":0.2521304147607955,
+       "Nucleotide GTR":0.2480198736772598,
+       "RELAX alternative":0.3426997068768813,
+       "RELAX null":0.2931467439343907,
+       "RELAX partitioned descriptive":0.3469082289876269,
+       "k (general descriptive)":2.852150041266453,
        "original name":"Cow"
       },
      "Horse":{
-       "General descriptive":0.2802176313870697,
-       "MG94xREV with separate rates for branch sets":0.2158304510870495,
-       "Nucleotide GTR":0.2090310577070883,
-       "RELAX alternative":0.3058487498567987,
-       "RELAX null":0.2559911331878715,
-       "RELAX partitioned descriptive":0.3034694616209482,
-       "k (general descriptive)":1.926646959057857,
+       "General descriptive":0.2804279827409984,
+       "MG94xREV with separate rates for branch sets":0.2158535884657318,
+       "Nucleotide GTR":0.2090998951755368,
+       "RELAX alternative":0.3058441352816696,
+       "RELAX null":0.2546949756245578,
+       "RELAX partitioned descriptive":0.3035514182923183,
+       "k (general descriptive)":1.929916608813313,
        "original name":"Horse"
       },
      "Human":{
@@ -59,101 +59,101 @@
        "RELAX alternative":0,
        "RELAX null":0,
        "RELAX partitioned descriptive":0,
-       "k (general descriptive)":1.462532487172471,
+       "k (general descriptive)":1.485684693044203,
        "original name":"Human"
       },
      "Mouse":{
-       "General descriptive":0.1307950021191255,
-       "MG94xREV with separate rates for branch sets":0.1197727080219867,
-       "Nucleotide GTR":0.1180171198334285,
-       "RELAX alternative":0.1346501492117481,
-       "RELAX null":0.1468861666244963,
-       "RELAX partitioned descriptive":0.1475623398849678,
-       "k (general descriptive)":0.4639609139295889,
+       "General descriptive":0.1308809509233143,
+       "MG94xREV with separate rates for branch sets":0.1197584101055861,
+       "Nucleotide GTR":0.1181058300538561,
+       "RELAX alternative":0.1346294129227689,
+       "RELAX null":0.1438267359449897,
+       "RELAX partitioned descriptive":0.148454172127534,
+       "k (general descriptive)":0.4625550584398252,
        "original name":"Mouse"
       },
      "Node1":{
-       "General descriptive":0.350050900813081,
-       "MG94xREV with separate rates for branch sets":0.2857356440257563,
-       "Nucleotide GTR":0.2767237570684924,
-       "RELAX alternative":0.3856490868629754,
-       "RELAX null":0.4521046025119397,
-       "RELAX partitioned descriptive":0.4358952685746469,
-       "k (general descriptive)":0.458870761901378
+       "General descriptive":0.3500691487967139,
+       "MG94xREV with separate rates for branch sets":0.2856782993656827,
+       "Nucleotide GTR":0.2767105173979571,
+       "RELAX alternative":0.385503346940632,
+       "RELAX null":0.4352096867868785,
+       "RELAX partitioned descriptive":0.4379872513902164,
+       "k (general descriptive)":0.4572754180074107
       },
      "Node12":{
-       "General descriptive":0.01766384491594095,
-       "MG94xREV with separate rates for branch sets":0.01800001211221997,
-       "Nucleotide GTR":0.01784803874223016,
-       "RELAX alternative":0.01835132674304535,
-       "RELAX null":0.0182458522959868,
-       "RELAX partitioned descriptive":0.01878351896299688,
-       "k (general descriptive)":0.1241597340554799
+       "General descriptive":0.01767932040676307,
+       "MG94xREV with separate rates for branch sets":0.01800350744117403,
+       "Nucleotide GTR":0.01784222107494562,
+       "RELAX alternative":0.01834159481548459,
+       "RELAX null":0.01822563245625142,
+       "RELAX partitioned descriptive":0.01881534539472323,
+       "k (general descriptive)":0.1240073621579099
       },
      "Node2":{
-       "General descriptive":0.05771641706257456,
-       "MG94xREV with separate rates for branch sets":0.06169547093990335,
-       "Nucleotide GTR":0.06613162123865737,
-       "RELAX alternative":0.05450381496370671,
-       "RELAX null":0.06144358908741494,
-       "RELAX partitioned descriptive":0.05974179966710006,
-       "k (general descriptive)":0.5400661932123572
+       "General descriptive":0.05767151047612454,
+       "MG94xREV with separate rates for branch sets":0.06170856993599769,
+       "Nucleotide GTR":0.06614755778044307,
+       "RELAX alternative":0.0544792799094392,
+       "RELAX null":0.06013052353393462,
+       "RELAX partitioned descriptive":0.0601550105387935,
+       "k (general descriptive)":0.5400834620465133
       },
      "Node3":{
-       "General descriptive":0.133048972566238,
-       "MG94xREV with separate rates for branch sets":0.09736816312927643,
-       "Nucleotide GTR":0.09886326330774685,
-       "RELAX alternative":0.1168284793254293,
-       "RELAX null":0.1276889506286756,
-       "RELAX partitioned descriptive":0.1195376339442456,
-       "k (general descriptive)":1.980345386854111
+       "General descriptive":0.1330088052861041,
+       "MG94xREV with separate rates for branch sets":0.09733132151710643,
+       "Nucleotide GTR":0.09883748387954429,
+       "RELAX alternative":0.1169235247351394,
+       "RELAX null":0.1263887172366205,
+       "RELAX partitioned descriptive":0.1196402015693241,
+       "k (general descriptive)":1.977892771876671
       },
      "Node8":{
-       "General descriptive":0.1404364853762839,
-       "MG94xREV with separate rates for branch sets":0.1092041281639667,
-       "Nucleotide GTR":0.106239268140425,
-       "RELAX alternative":0.1283918913740865,
-       "RELAX null":0.1343238120118072,
-       "RELAX partitioned descriptive":0.1363833239244288,
-       "k (general descriptive)":2.210166852936262
+       "General descriptive":0.140412283431793,
+       "MG94xREV with separate rates for branch sets":0.1091939823455765,
+       "Nucleotide GTR":0.1062201244057951,
+       "RELAX alternative":0.1284192265733904,
+       "RELAX null":0.1334227466998376,
+       "RELAX partitioned descriptive":0.1367904558404228,
+       "k (general descriptive)":2.206967022203622
       },
      "Node9":{
-       "General descriptive":0.02665050120918479,
-       "MG94xREV with separate rates for branch sets":0.02578196090462333,
-       "Nucleotide GTR":0.02566573875750134,
-       "RELAX alternative":0.02679622227446188,
-       "RELAX null":0.02754241929890747,
-       "RELAX partitioned descriptive":0.0274479920792393,
-       "k (general descriptive)":0.0733131770696667
+       "General descriptive":0.02664133794298214,
+       "MG94xREV with separate rates for branch sets":0.02578742148415842,
+       "Nucleotide GTR":0.02567813733543303,
+       "RELAX alternative":0.02680940150436639,
+       "RELAX null":0.0273694783141817,
+       "RELAX partitioned descriptive":0.02747376898615263,
+       "k (general descriptive)":0.07343731037788495
       },
      "Pig":{
-       "General descriptive":0.2104601216238473,
-       "MG94xREV with separate rates for branch sets":0.1902977811335351,
-       "Nucleotide GTR":0.1871893456388788,
-       "RELAX alternative":0.19752905148822,
-       "RELAX null":0.2165309177979844,
-       "RELAX partitioned descriptive":0.2074828949843082,
-       "k (general descriptive)":1.577441472516679,
+       "General descriptive":0.210591346560755,
+       "MG94xREV with separate rates for branch sets":0.1903463787974325,
+       "Nucleotide GTR":0.1871390433004313,
+       "RELAX alternative":0.1974790507889271,
+       "RELAX null":0.2130024973755621,
+       "RELAX partitioned descriptive":0.2084407457285946,
+       "k (general descriptive)":1.581210670484469,
        "original name":"Pig"
       },
      "Rat":{
-       "General descriptive":0.07164210204456434,
-       "MG94xREV with separate rates for branch sets":0.06709541225974219,
-       "Nucleotide GTR":0.06661283005976348,
-       "RELAX alternative":0.07247047023746757,
-       "RELAX null":0.07343093575256582,
-       "RELAX partitioned descriptive":0.07560655472076994,
-       "k (general descriptive)":1.318174884032695,
+       "General descriptive":0.07157977734335202,
+       "MG94xREV with separate rates for branch sets":0.06709765698107663,
+       "Nucleotide GTR":0.06661490534189227,
+       "RELAX alternative":0.07252374836036582,
+       "RELAX null":0.0734705682786943,
+       "RELAX partitioned descriptive":0.0757525093290258,
+       "k (general descriptive)":1.316568267879453,
        "original name":"Rat"
       },
      "RhMonkey":{
-       "General descriptive":0.003674505194636419,
-       "MG94xREV with separate rates for branch sets":0.003716165486244973,
-       "Nucleotide GTR":0.003775170135617877,
-       "RELAX alternative":0.003636176595806718,
-       "RELAX null":0.003665938723426083,
-       "RELAX partitioned descriptive":0.003624376345656283,
-       "k (general descriptive)":5.171610533872274,
+       "General descriptive":0.003672848089716511,
+       "MG94xREV with separate rates for branch sets":0.003717350789869306,
+       "Nucleotide GTR":0.003778804730491441,
+       "RELAX alternative":0.003633278464154418,
+       "RELAX null":0.003661271320845124,
+       "RELAX partitioned descriptive":0.003625957794514879,
+       "k (general descriptive)":5.196295069596697,
        "original name":"RhMonkey"
       }
     },
@@ -202,21 +202,21 @@
   },
  "fits":{
    "General descriptive":{
-     "AIC-c":6945.891353881681,
-     "Log Likelihood":-3420.486931066253,
+     "AIC-c":6945.892677835464,
+     "Log Likelihood":-3420.487593043145,
      "Rate Distributions":{
        "Shared":{
          "0":{
-           "omega":2.202835393423959e-18,
-           "proportion":0.4487473029633234
+           "omega":2.201451464048879e-18,
+           "proportion":0.3073650505039141
           },
          "1":{
-           "omega":2.202835393423959e-18,
-           "proportion":0.09729227592412616
+           "omega":2.201451464048879e-18,
+           "proportion":0.2383891488636319
           },
          "2":{
-           "omega":2.202835210940273,
-           "proportion":0.4539604211125504
+           "omega":2.201451281679838,
+           "proportion":0.4542458006324541
           }
         }
       },
@@ -224,7 +224,7 @@
      "estimated parameters":51
     },
    "MG94xREV with separate rates for branch sets":{
-     "AIC-c":6987.565999172035,
+     "AIC-c":6987.566513560764,
      "Equilibrium frequencies":      [
 [0.04876086397632926],
       [0.03982224127745371],
@@ -288,68 +288,68 @@
       [0.01417464125436193],
       [0.01189287130232129] 
       ],
-     "Log Likelihood":-3461.208149286616,
+     "Log Likelihood":-3461.208406480981,
      "Rate Distributions":{
        "non-synonymous/synonymous rate ratio for *Reference*":        [
-[0.7682335289209781, 1] 
+[0.7685912547191639, 1] 
         ],
        "non-synonymous/synonymous rate ratio for *Test*":        [
-[1.605439824256426, 1] 
+[1.603198088111489, 1] 
         ]
       },
      "display order":1,
      "estimated parameters":32
     },
    "Nucleotide GTR":{
-     "AIC-c":7112.857310169033,
+     "AIC-c":7112.857288723968,
      "Equilibrium frequencies":      [
 [0.3592490842490842],
       [0.181959706959707],
       [0.240018315018315],
       [0.2187728937728937] 
       ],
-     "Log Likelihood":-3532.32122446679,
+     "Log Likelihood":-3532.321213744258,
      "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
+       "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
+       "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
+       "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
+       "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
       },
      "display order":0,
      "estimated parameters":24
     },
    "RELAX alternative":{
-     "AIC-c":6931.922980697387,
-     "Log Likelihood":-3429.234812770952,
+     "AIC-c":6931.926773483473,
+     "Log Likelihood":-3429.236709163995,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":1.762268314739328e-19,
-           "proportion":0.4504132080156107
+           "omega":1.761161171239182e-19,
+           "proportion":0.2691773911207853
           },
          "1":{
-           "omega":1.762268314739328e-19,
-           "proportion":0.08749553114962015
+           "omega":1.762922332410267e-19,
+           "proportion":0.2692122656891806
           },
          "2":{
-           "omega":2.19971015101232,
-           "proportion":0.4620912608347691
+           "omega":2.208286837998088,
+           "proportion":0.4616103431900341
           }
         },
        "Test":{
          "0":{
-           "omega":1.054840660215593e-44,
-           "proportion":0.4504132080156107
+           "omega":1.673670300056362e-44,
+           "proportion":0.2691773911207853
           },
          "1":{
-           "omega":1.054840660215593e-44,
-           "proportion":0.08749553114962015
+           "omega":1.677579612236672e-44,
+           "proportion":0.2692122656891806
           },
          "2":{
-           "omega":6.350765030542244,
-           "proportion":0.4620912608347691
+           "omega":6.354762788556926,
+           "proportion":0.4616103431900341
           }
         }
       },
@@ -357,35 +357,35 @@
      "estimated parameters":36
     },
    "RELAX null":{
-     "AIC-c":6946.046672507471,
-     "Log Likelihood":-3437.336313352972,
+     "AIC-c":6946.648596594286,
+     "Log Likelihood":-3437.63727539638,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":0.1150006822953211,
-           "proportion":0.542405144031307
+           "omega":1.408928936991542e-20,
+           "proportion":0.265244047162938
           },
          "1":{
-           "omega":0.2401508033814633,
-           "proportion":0.08223353569636478
+           "omega":1.410337865928411e-20,
+           "proportion":0.28512630848952
           },
          "2":{
-           "omega":3.69263720947284,
-           "proportion":0.3753613202723282
+           "omega":3.213510017765925,
+           "proportion":0.4496296443475419
           }
         },
        "Test":{
          "0":{
-           "omega":0.1150006822953211,
-           "proportion":0.542405144031307
+           "omega":1.408928936991542e-20,
+           "proportion":0.265244047162938
           },
          "1":{
-           "omega":0.2401508033814633,
-           "proportion":0.08223353569636478
+           "omega":1.410337865928411e-20,
+           "proportion":0.28512630848952
           },
          "2":{
-           "omega":3.69263720947284,
-           "proportion":0.3753613202723282
+           "omega":3.213510017765925,
+           "proportion":0.4496296443475419
           }
         }
       },
@@ -393,35 +393,35 @@
      "estimated parameters":35
     },
    "RELAX partitioned descriptive":{
-     "AIC-c":6937.04707353565,
-     "Log Likelihood":-3427.626871923648,
+     "AIC-c":6937.049237937651,
+     "Log Likelihood":-3427.627954124649,
      "Rate Distributions":{
        "Reference":{
          "0":{
-           "omega":0.1943306885168281,
-           "proportion":0.3359458135547653
+           "omega":0.1847557016619168,
+           "proportion":0.4766160247339328
           },
          "1":{
-           "omega":0.2607558478587815,
-           "proportion":0.4332550437039296
+           "omega":0.3367540359539261,
+           "proportion":0.3005513276312735
           },
          "2":{
-           "omega":4.134271224300374,
-           "proportion":0.2307991427413052
+           "omega":4.272816072857538,
+           "proportion":0.2228326476347937
           }
         },
        "Test":{
          "0":{
-           "omega":0,
-           "proportion":0.4753488415962343
+           "omega":1.127143149593234e-21,
+           "proportion":0.2367540589657237
           },
          "1":{
-           "omega":0,
-           "proportion":0.03858318603767072
+           "omega":1.128270292740756e-21,
+           "proportion":0.2771164325302933
           },
          "2":{
-           "omega":6.017221959238516,
-           "proportion":0.486067972366095
+           "omega":6.023626417874829,
+           "proportion":0.4861295085039831
           }
         }
       },
@@ -430,7 +430,7 @@
     }
   },
  "input":{
-   "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.fasta",
+   "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta",
    "number of sequences":10,
    "number of sites":187,
    "partition count":1,
@@ -438,10 +438,11 @@
      "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)"
     }
   },
+ "runtime":"2.5.32",
  "test results":{
-   "LRT":16.20300116404087,
-   "p-value":5.690389451429301e-05,
-   "relaxation or intensification parameter":2.344938789085876
+   "LRT":16.80113246476958,
+   "p-value":4.150852429507523e-05,
+   "relaxation or intensification parameter":2.334214628944839
   },
  "tested":{
    "0":{
@@ -466,11 +467,11 @@
  "timers":{
    "General descriptive model fitting":{
      "order":2,
-     "timer":132
+     "timer":127
     },
    "Overall":{
      "order":0,
-     "timer":324
+     "timer":396
     },
    "Preliminary model fitting":{
      "order":1,
@@ -478,15 +479,15 @@
     },
    "RELAX alternative model fitting":{
      "order":3,
-     "timer":65
+     "timer":103
     },
    "RELAX null model fitting":{
      "order":4,
-     "timer":66
+     "timer":41
     },
    "RELAX partitioned descriptive":{
      "order":5,
-     "timer":53
+     "timer":116
     }
   }
 }
\ No newline at end of file