hyphy_slac: test-data/summary/nsp7.FADE.json comparison

comparison test-data/summary/nsp7.FADE.json @ 27:6fc5626996b4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"

author	iuc
date	Wed, 09 Jun 2021 07:07:57 +0000
parents
children

comparison

equal deleted inserted replaced

-:0c6724c345d9
+:6fc5626996b4
+{
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+}
+},
+"headers":    [
+["rate", "Mean posterior relative rate at a site"],
+["bias", "Mean posterior bias parameter at a site"],
+["Prob[bias>0]", "Posterior probability of substitution bias"],
+["BayesFactor[bias>0]", "Empiricial Bayes Factor for substitution bias"]
+]
+},
+"analysis":{
+"authors":"Sergei L Kosakovsky Pond",
+"citation":"TBD",
+"contact":"spond@temple.edu",
+"info":"FADE (FUBAR Approach to Directional Evolution) is a fast method to test whether or not a subset of sites in a protein alignment\n                            evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model.\n                            FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.",
+"requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})",
+"version":"0.2"
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+}
+},
+"settings":{
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+"burn-in":1000000,
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+"chains":1,
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+"grid size":20,
+"method":"Variational-Bayes",
+"samples":100
+},
+"site annotations":{
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+"Substitutions":"Substitution history on selected branches"
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+["K11", ""],
+["F1,L10", ""],
+["C11", ""],
+["E11", ""],
+["D1,E10", "E->D(1)"],
+["I1,M9,V1", "M->V(1)"],
+["L11", ""],
+["D11", ""],
+["N11", ""],
+["R11", ""],
+["A11", ""],
+["I1,T10", ""],
+["L11", ""],
+["Q11", ""]
+]
+}
+},
+"tested":{
+"0":{
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+"EPI_ISL_1415264_HCOV_19_INDIA_MH_NCCS_128864_2021":"test",
+"EPI_ISL_1415273_HCOV_19_INDIA_MH_NCCS_87216_2021":"test",
+"EPI_ISL_1416968_HCOV_19_GUADELOUPE_IPP06229_2021":"test",
+"EPI_ISL_1564187_HCOV_19_ENGLAND_CAMC_14D5BFD_2021":"test",
+"EPI_ISL_1583966_HCOV_19_ENGLAND_CAMC_14D1B4C_2021":"test",
+"EPI_ISL_1635400_HCOV_19_SCOTLAND_CAMC_14DEDB2_2021":"test",
+"EPI_ISL_1641831_HCOV_19_GERMANY_BY_RKI_I_076082_2021":"test",
+"EPI_ISL_1648157_HCOV_19_USA_CA_CDC_QDX23571833_2021":"test",
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+"GB_MW277234_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC15990_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW277460_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC12022_2020_SEGMENT_NULL_HOST_HUMAN":"background",
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+"GB_MW306408_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_12385_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW320996_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC17273_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW321295_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC17192_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW332236_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_RUS_2272_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW338802_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_VA_DCLS_2062_2020_SEGMENT_NULL_HOST_HUMAN":"background",
+"GB_MW341806_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_IL_UW_1937_2020_SEGMENT_NULL_HOST_HUMAN":"background",
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Mercurial > repos > iuc > hyphy_slac

comparison test-data/summary/nsp7.FADE.json @ 27:6fc5626996b4 draft