diff test-data/FEL/gene2.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FEL/gene2.json	Thu Dec 04 15:05:26 2025 +0000
@@ -0,0 +1,345 @@
+{
+ "MLE":{
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+   "headers":    [
+["alpha", "Synonymous substitution rate at a site"],
+    ["beta", "Non-synonymous substitution rate at a site"],
+    ["alpha=beta", "The rate estimate under the neutral model"],
+    ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
+    ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
+    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
+    ]
+  },
+ "analysis":{
+   "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
+   "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
+   "contact":"[e-mail]",
+   "info":"FEL (Fixed Effects Likelihood)\n    estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n    uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n    The estimates aggregate information over all branches,\n    so the signal is derived from\n    pervasive diversification or conservation. A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing.\n    Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis. Version 2.5 adds MH support.\n    ",
+   "requirements":"in-frame codon alignment and a phylogenetic tree",
+   "settings":{
+     "ci":0,
+     "multihit":"None",
+     "pvalue":0.1,
+     "resample":0,
+     "site-filter":{
+       "site-filter":null,
+       "site-save-filter":null
+      },
+     "srv":1
+    },
+   "version":"2.5"
+  },
+ "branch attributes":{
+   "0":{
+     "Node2":{
+       "Global MG94xREV":0.01555447631320992,
+       "Nucleotide GTR":0.01391650578382423
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+     "Node3":{
+       "Global MG94xREV":0.007028865074476463,
+       "Nucleotide GTR":0.007313844682570613
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+       "Global MG94xREV":0.006626243690924009,
+       "Nucleotide GTR":0.006196659368038242
+      },
+     "PP563830_1_2023_09_02":{
+       "Global MG94xREV":0,
+       "Nucleotide GTR":1e-06,
+       "original name":"PP563830_1_2023_09_02"
+      },
+     "PP563831_1_2023_08_29":{
+       "Global MG94xREV":0.003308232804180055,
+       "Nucleotide GTR":0.003339882520232537,
+       "original name":"PP563831_1_2023_08_29"
+      },
+     "PP563832_1_2023_08_28":{
+       "Global MG94xREV":0.003305901719100713,
+       "Nucleotide GTR":0.003342518270787742,
+       "original name":"PP563832_1_2023_08_28"
+      },
+     "PP563838_1_2023_09_30":{
+       "Global MG94xREV":0.003316292450534825,
+       "Nucleotide GTR":0.003339882520180704,
+       "original name":"PP563838_1_2023_09_30"
+      },
+     "PP563839_1_2023_09_29":{
+       "Global MG94xREV":0,
+       "Nucleotide GTR":1e-06,
+       "original name":"PP563839_1_2023_09_29"
+      },
+     "PP563845_1_2023_10_22":{
+       "Global MG94xREV":0.005918187425081579,
+       "Nucleotide GTR":0.007157676157708746,
+       "original name":"PP563845_1_2023_10_22"
+      },
+     "PP564823_1_2023_10_06":{
+       "Global MG94xREV":0.04453027608174031,
+       "Nucleotide GTR":0.04195089101557686,
+       "original name":"PP564823_1_2023_10_06"
+      }
+    },
+   "attributes":{
+     "Global MG94xREV":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      }
+    }
+  },
+ "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]
+      ],
+     "name":"fel.filter.default"
+    }
+  },
+ "fits":{
+   "Global MG94xREV":{
+     "AIC-c":1098.164180855893,
+     "Equilibrium frequencies":      [
+[0.04022787530103862],
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+      [0.03425741450905353],
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+      [0.02335376908798366],
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+      [0.0132212670023302],
+      [0.02341317633368553],
+      [0.009744994946783913]
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+     "Log Likelihood":-522.0389997890163,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *background*":        [
+[0.2130893675277186, 1]
+        ],
+       "non-synonymous/synonymous rate ratio for *test*":        [
+[0.05367140804417245, 1]
+        ]
+      },
+     "display order":1,
+     "estimated parameters":26
+    },
+   "Nucleotide GTR":{
+     "AIC-c":1130.795872905925,
+     "Equilibrium frequencies":      [
+[0.3347619047619048],
+      [0.2033333333333333],
+      [0.2466666666666667],
+      [0.2152380952380952]
+      ],
+     "Log Likelihood":-546.2152441452704,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0,
+       "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+       "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+       "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
+      },
+     "display order":0,
+     "estimated parameters":19
+    }
+  },
+ "input":{
+   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/66/caf0861a1e46548e7f15d9b82a4920/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
+   "number of sequences":7,
+   "number of sites":100,
+   "partition count":1,
+   "trees":{
+     "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
+    }
+  },
+ "runtime":"2.5.73",
+ "tested":{
+   "0":{
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "PP563830_1_2023_09_02":"background",
+     "PP563831_1_2023_08_29":"background",
+     "PP563832_1_2023_08_28":"background",
+     "PP563838_1_2023_09_30":"background",
+     "PP563839_1_2023_09_29":"background",
+     "PP563845_1_2023_10_22":"background",
+     "PP564823_1_2023_10_06":"background"
+    }
+  },
+ "timers":{
+   "FEL analysis":{
+     "order":2,
+     "timer":4
+    },
+   "Model fitting":{
+     "order":1,
+     "timer":1
+    },
+   "Total time":{
+     "order":0,
+     "timer":5
+    }
+  }
+}