Mercurial > repos > iuc > hyphy_slac
comparison test-data/bgm-out1.json @ 2:a603e2f909e5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author | iuc |
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date | Thu, 13 Feb 2020 15:03:50 -0500 |
parents | c2bed8cc8fc1 |
children |
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1:c2bed8cc8fc1 | 2:a603e2f909e5 |
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1 { | 1 { |
2 "MLE":{ | 2 "MLE":{ |
3 "content": [ | 3 "content": [ |
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280 ], | 40 ], |
281 "headers": [ | 41 "headers": [ |
282 ["Site 1", "Index of site 1"], | 42 ["Site 1", "Index of site 1"], |
283 ["Site 2", "Index of site 2"], | 43 ["Site 2", "Index of site 2"], |
284 ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], | 44 ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], |
298 "version":"1.1" | 58 "version":"1.1" |
299 }, | 59 }, |
300 "branch attributes":{ | 60 "branch attributes":{ |
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308 "Chimp":{ | 68 "Chimp":{ |
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326 "Node12":{ | 86 "Node12":{ |
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341 "Pig":{ | 101 "Pig":{ |
342 "models.DNA.GTR.ModelDescription":0 | 102 "models.codon.MG_REV.ModelDescription":0 |
343 }, | 103 }, |
344 "Rat":{ | 104 "Rat":{ |
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346 }, | 106 }, |
347 "RhMonkey":{ | 107 "RhMonkey":{ |
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349 } | 109 } |
350 }, | 110 }, |
351 "attributes":{ | 111 "attributes":{ |
352 "models.DNA.GTR.ModelDescription":{ | 112 "models.codon.MG_REV.ModelDescription":{ |
353 "attribute type":"branch length", | 113 "attribute type":"branch length", |
354 "display order":0 | 114 "display order":0 |
355 } | 115 } |
356 } | 116 } |
357 }, | 117 }, |
358 "data partitions":{ | 118 "data partitions":{ |
359 "0":{ | 119 "0":{ |
360 "coverage": [ | 120 "coverage": [ |
361 [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] | 121 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9] |
362 ], | 122 ], |
363 "name":"bgm.filter.default" | 123 "name":"bgm.filter.default" |
364 } | 124 } |
365 }, | 125 }, |
366 "fits":{ | 126 "fits":{ |
367 "models.DNA.GTR.ModelDescription":{ | 127 "models.codon.MG_REV.ModelDescription":{ |
368 "AIC-c":472.7691802214979, | 128 "AIC-c":508.3788244913426, |
369 "Log Likelihood":-210.2027719289308, | 129 "Log Likelihood":-208.6011769515537, |
370 "Rate Distributions":null, | 130 "Rate Distributions":null, |
371 "display order":0, | 131 "display order":0, |
372 "estimated parameters":24 | 132 "estimated parameters":31 |
373 } | 133 } |
374 }, | 134 }, |
375 "input":{ | 135 "input":{ |
376 "datatype":"nucleotide", | 136 "datatype":"codon", |
377 "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa", | 137 "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa", |
378 "number of sequences":10, | 138 "number of sequences":10, |
379 "number of sites":30, | 139 "number of sites":10, |
380 "trees":{ | 140 "trees":{ |
381 "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)" | 141 "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)" |
382 } | 142 } |
383 }, | 143 }, |
384 "settings":{ | 144 "settings":{ |
385 "burn-in":10000, | 145 "burn-in":10000, |
386 "data-type":"nucleotide", | 146 "data-type":"codon", |
387 "max-parents":1, | 147 "max-parents":1, |
388 "min-subs":1, | 148 "min-subs":1, |
389 "samples":100, | 149 "samples":100, |
390 "steps":100000, | 150 "steps":100000, |
391 "threshold":0.5 | 151 "threshold":0.5 |
392 }, | 152 }, |
393 "tested":0, | 153 "tested":0, |
394 "timers":{ | 154 "timers":{ |
395 "Baseline fit":{ | 155 "Baseline fit":{ |
396 "order":1, | 156 "order":1, |
397 "timer":0 | 157 "timer":3 |
398 }, | 158 }, |
399 "Network inference":{ | 159 "Network inference":{ |
400 "order":2, | 160 "order":2, |
401 "timer":1 | 161 "timer":0 |
402 }, | 162 }, |
403 "Overall":{ | 163 "Overall":{ |
404 "order":0, | 164 "order":0, |
405 "timer":1 | 165 "timer":3 |
406 } | 166 } |
407 } | 167 } |
408 } | 168 } |