| Previous changeset 31:26de3a7b1cb9 (2021-10-05) Next changeset 33:212c958f6cee (2022-03-30) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc" |
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modified:
hyphy_absrel.xml macros.xml test-data/busted-in2.nex test-data/busted-out2-1.json test-data/busted-out2-2.json |
| b |
| diff -r 26de3a7b1cb9 -r 3f59ebfbfe3d hyphy_absrel.xml --- a/hyphy_absrel.xml Tue Oct 05 05:11:08 2021 +0000 +++ b/hyphy_absrel.xml Sat Nov 27 11:25:19 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1" profile="19.09"> +<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09"> <description>adaptive Branch Site Random Effects Likelihood</description> <expand macro="bio_tools"/> <macros> @@ -20,7 +20,6 @@ ]]></command> <inputs> <expand macro="inputs"/> - <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/> <expand macro="gencode"/> <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions"> <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option> |
| b |
| diff -r 26de3a7b1cb9 -r 3f59ebfbfe3d macros.xml --- a/macros.xml Tue Oct 05 05:11:08 2021 +0000 +++ b/macros.xml Sat Nov 27 11:25:19 2021 +0000 |
| b |
| @@ -144,10 +144,10 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.31</token> + <token name="@TOOL_VERSION@">2.5.31</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">hyphy</requirement> + <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> <yield/> </requirements> </xml> |
| b |
| diff -r 26de3a7b1cb9 -r 3f59ebfbfe3d test-data/busted-in2.nex --- a/test-data/busted-in2.nex Tue Oct 05 05:11:08 2021 +0000 +++ b/test-data/busted-in2.nex Sat Nov 27 11:25:19 2021 +0000 |
| b |
| @@ -26,5 +26,5 @@ END; BEGIN TREES; - TREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160)); + TREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160{B_US_90_WEAU160_BRANCH})); END; |
| b |
| diff -r 26de3a7b1cb9 -r 3f59ebfbfe3d test-data/busted-out2-1.json --- a/test-data/busted-out2-1.json Tue Oct 05 05:11:08 2021 +0000 +++ b/test-data/busted-out2-1.json Sat Nov 27 11:25:19 2021 +0000 |
| [ |
| b'@@ -1,21 +1,21 @@\n {\n "Evidence Ratios":{\n "constrained": [\n-[0.935557169656361, 0.9478485707814517, 0.9365713272643597, 0.9348516866501475, 0.9478485707814517, 0.9470782825238451, 0.9404255507056813, 0.9445269614625446, 0.9357171171944089, 0.9445269614625446, 0.951038343352286, 0.9642191069363555, 0.9509681609268663, 0.9357171171944089, 0.9365508162861411, 0.9330337048596494, 0.9453769311406178, 0.9354507653189286, 0.9357171171944089, 0.951038343352286, 0.944959794342383, 0.951038343352286, 0.9554450473318812, 0.957741198595587, 0.9357223141306646, 0.9635859922205572, 0.9400812190552175, 0.9471227276423632, 0.9471155585144405, 0.951038343352286, 0.9425085292914046, 0.951038343352286, 0.9382075921692818, 0.9681439336221066, 9.055411306947674, 0.9467899324264936, 0.9478485707814517, 0.9398061397692539, 1.097085569751409, 1.371682580705311, 1.704754646360477, 0.9467899324264936, 0.9509681609268663, 0.9467899324264936, 0.9364415899930733, 0.951038343352286, 0.9478485707814517, 0.9525827524658199, 1.146813959542357, 0.9478485707814517, 0.9362276370626634, 0.9348516866501475, 0.9467899324264936, 0.9486832156560699, 0.9357171171944089, 0.9541686971206805, 0.9484511531422709, 0.9404255507056813, 0.9357171171944089, 1.072863229391129, 0.947891315956519, 0.938167627826613, 0.9425085292914046, 0.9509681609268663, 0.951038343352286, 0.9514408733975561, 0.9395660064639854, 0.9365128450433999, 0.9404014893688138, 0.9514344449206511, 0.957741198595587, 0.9388792918800136, 0.951038343352286, 0.9642191069363555, 0.9445269614625446, 0.9453769311406178, 0.9418928080136506, 0.9388792918800136, 0.9467899324264936, 0.9399880829471382, 0.9484511531422709, 0.9509681609268663, 1.153990916133998, 0.9404255507056813, 0.9554450473318812, 0.9412338215355154, 0.942333955072914, 0.957741198595587, 0.9470815762343416, 0.9449667231570663, 0.9557119925844111, 0.9676532717080474, 0.9365050172103501, 0.9425085292914046, 0.9357012899378949, 0.9407207493748144, 0.9348483936808639, 1.953541836729934, 0.9362670029301522, 0.9644232801771531, 0.9515108647313498, 0.9509681609268663, 1.168382764503998, 0.9515108647313498, 0.949860271872106, 1.047791522454514, 0.9400812190552175, 0.9445269614625446, 0.9566068656126535, 0.9453769311406178, 0.9434809129833114, 0.936045980720387, 0.9455636023716772, 0.9382075921692818, 0.9549292932384192, 0.9479532753114727, 0.949860271872106, 1.071924199060109, 0.9347728559684337, 0.9642191069363555, 61.30480048708166, 1.392589724214399, 1.068829280572215, 0.9452448851782124, 0.9383322213205718, 0.9520356968106081, 0.9548771157697881, 0.9403109573428395, 0.9383425168225155, 0.9481200597562297, 0.9401597754529221, 0.9425085292914046, 1.081655864332756, 0.9365128450433999, 0.958884569235499, 0.9416389648192759, 0.9484511531422709, 0.9474364959906919, 0.9400812190552175, 0.9357171171944089, 1.013189964747481, 0.9478485707814517, 0.939061940389555, 0.9549292932384192, 0.9544426850176303, 0.9541087300514087, 0.9484511531422709, 0.9456450378925056, 0.9399863915898927, 0.9357147779844784, 0.9552428339477506, 0.9365032950653777, 0.957741198595587, 0.951038343352286, 0.9364880871021735, 0.949860271872106, 0.9357012899378949, 0.9382075921692818, 0.9425085292914046, 0.9418928080136506, 0.9554450473318812, 0.9365128450433999, 0.9333687495168144, 0.9330337048596494, 1.030183566875361, 0.951038343352286, 0.9530190340820841, 0.9642191069363555, 0.9471668565289959, 0.9348308160631009, 0.947891315956519, 1.060517303033454, 0.951038343352286, 0.9554450473318812, 0.9484511531422709, 0.9357171171944089, 1.428578774814407, 1.256482256153546, 1.21301128797193, 0.9447052888159178, 0.9549292932384192, 0.9554450473318812, 0.9541087300514087, 0.9330337048596494, 0.9453769311406178, 0.9453769311406178, 0.9635859922205572, 0.9549292932384192, 0.9445269614625446, 0.9364880871021735, 0.9422504512769631, 0.9408248422372665, 0.9642191069363555, 0.9471081975229871, 0.9425085292914046, 0.9362670029301522, 0.9544426850176303, 0.9407207493748144, 0.9390630876730207,'..b'on":0.02050403204170275\n }\n }\n },\n "display order":3,\n- "estimated parameters":31\n+ "estimated parameters":36\n },\n "MG94xREV with separate rates for branch sets":{\n- "AIC-c":6408.899382280021,\n+ "AIC-c":6410.490466219016,\n "Equilibrium frequencies": [\n [0.07535940345366139],\n [0.01443006409728228],\n@@ -235,14 +249,17 @@\n [0.0132120929750345],\n [0.01338903305480236] \n ],\n- "Log Likelihood":-3176.217093030587,\n+ "Log Likelihood":-3175.995949441886,\n "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *background*": [\n+[0.2379324068936849, 1] \n+ ],\n "non-synonymous/synonymous rate ratio for *test*": [\n-[0.231720664913378, 1] \n+[0.1777604776475358, 1] \n ]\n },\n "display order":1,\n- "estimated parameters":28\n+ "estimated parameters":29\n },\n "Nucleotide GTR":{\n "AIC-c":6683.094244259512,\n@@ -265,30 +282,44 @@\n "estimated parameters":21\n },\n "Unconstrained model":{\n- "AIC-c":6391.938375474656,\n- "Log Likelihood":-3163.666348620609,\n+ "AIC-c":6400.149223170942,\n+ "Log Likelihood":-3162.670820660715,\n "Rate Distributions":{\n+ "Background":{\n+ "0":{\n+ "omega":0.1679188282558003,\n+ "proportion":0.8207520434237199\n+ },\n+ "1":{\n+ "omega":0.2120937673953722,\n+ "proportion":0.1693698006934513\n+ },\n+ "2":{\n+ "omega":13.84252711122189,\n+ "proportion":0.00987815588282877\n+ }\n+ },\n "Test":{\n "0":{\n- "omega":0.1490485393860332,\n- "proportion":0.02658974082564446\n+ "omega":0.08367159828032572,\n+ "proportion":0.9533274940567786\n },\n "1":{\n- "omega":0.169565784922581,\n- "proportion":0.9641001770967245\n+ "omega":0.2493792697064242,\n+ "proportion":0.03716922067476962\n },\n "2":{\n- "omega":15.09387961636913,\n- "proportion":0.009310082077631076\n+ "omega":34.20463703717275,\n+ "proportion":0.009503285268451747\n }\n }\n },\n "display order":2,\n- "estimated parameters":32\n+ "estimated parameters":37\n }\n },\n "input":{\n- "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",\n+ "file name":"/tmp/tmpfzf3u9m4/job_working_directory/000/2/working/./input.nex",\n "number of sequences":8,\n "number of sites":440,\n "partition count":1,\n@@ -297,42 +328,42 @@\n }\n },\n "test results":{\n- "LRT":8.711160142067456,\n- "p-value":0.006417496108925114\n+ "LRT":3.465106677611402,\n+ "p-value":0.08841616008911996\n },\n "tested":{\n "0":{\n- "B_FR_83_HXB2":"test",\n- "B_US_83_RF":"test",\n- "B_US_86_JRFL":"test",\n+ "B_FR_83_HXB2":"background",\n+ "B_US_83_RF":"background",\n+ "B_US_86_JRFL":"background",\n "B_US_90_WEAU160":"test",\n- "D_CD_83_ELI":"test",\n- "D_CD_83_NDK":"test",\n- "D_CD_84_84ZR085":"test",\n- "D_UG_94_94UG114":"test",\n- "Node1":"test",\n- "Node10":"test",\n- "Node2":"test",\n- "Node3":"test",\n- "Node9":"test"\n+ "D_CD_83_ELI":"background",\n+ "D_CD_83_NDK":"background",\n+ "D_CD_84_84ZR085":"background",\n+ "D_UG_94_94UG114":"background",\n+ "Node1":"background",\n+ "Node10":"background",\n+ "Node2":"background",\n+ "Node3":"background",\n+ "Node9":"background"\n }\n },\n "timers":{\n "Constrained BUSTED model fitting":{\n "order":3,\n- "timer":23\n+ "timer":14\n },\n "Overall":{\n "order":0,\n- "timer":133\n+ "timer":60\n },\n "Preliminary model fitting":{\n "order":1,\n- "timer":4\n+ "timer":3\n },\n "Unconstrained BUSTED model fitting":{\n "order":2,\n- "timer":105\n+ "timer":40\n }\n }\n }\n\\ No newline at end of file\n' |
| b |
| diff -r 26de3a7b1cb9 -r 3f59ebfbfe3d test-data/busted-out2-2.json --- a/test-data/busted-out2-2.json Tue Oct 05 05:11:08 2021 +0000 +++ b/test-data/busted-out2-2.json Sat Nov 27 11:25:19 2021 +0000 |
| [ |
| b'@@ -26,63 +26,1730 @@\n END;\n \n BEGIN TREES;\n-\tTREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160));\n+\tTREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160{B_US_90_WEAU160_BRANCH}));\n END;\n \n BEGIN HYPHY;\n \n \n-global busted.test.bsrel_mixture_aux_0=0.9641001770967245;\n+global busted.background.bsrel_mixture_aux_0=0.1693698006934513;\n+busted.background.bsrel_mixture_aux_0:<1;\n+global busted.background.bsrel_mixture_aux_1=0.988107636959172;\n+busted.background.bsrel_mixture_aux_1:<1;\n+global busted.background.omega1=0.2120937673953722;\n+busted.background.omega1:<1;\n+global busted.background.omega2=0.1679188282558003;\n+busted.background.omega2:<1;\n+global busted.background.omega3=13.84252711122189;\n+global busted.test.theta_AT=0.08592789487428711;\n+global busted.test.theta_CG=0.3252168536335274;\n+global busted.test.theta_CT=1.270142771514482;\n+global busted.test.theta_AC=0.2087011772321373;\n+global busted.test.theta_GT=0.01381611313186033;\n+global busted.test.bsrel_mixture_aux_0=0.9533274940567786;\n busted.test.bsrel_mixture_aux_0:<1;\n-global busted.test.bsrel_mixture_aux_1=0.7406649580775059;\n+global busted.test.omega1=0.08367159828032572;\n+busted.test.omega1:<1;\n+global busted.test.bsrel_mixture_aux_1=0.7963836507940498;\n busted.test.bsrel_mixture_aux_1:<1;\n-global busted.test.omega1=0.169565784922581;\n-busted.test.omega1:<1;\n-global busted.test.omega2=0.1490485393860332;\n-busted.test.omega2:<1;\n-global busted.test.omega3=15.09387961636913;\n+global busted.test.omega3=34.20463703717275;\n busted.test.omega3:>1;\n busted.test.omega3:<10000000000;\n-global busted.test.theta_GT=0.02357543200455627;\n-global busted.test.theta_CT=1.263698936859757;\n-global busted.test.theta_AC=0.2111611676313184;\n-global busted.test.theta_CG=0.3198378552689968;\n-global busted.test.theta_AT=0.08720815485914278;\n+global busted.test.omega2=0.2493792697064242;\n+busted.test.omega2:<1;\n global busted.test.theta_AG:=1;\n+global busted.background.theta_AC:=busted.test.theta_AC;\n+global busted.background.theta_AG:=1;\n+global busted.background.theta_AT:=busted.test.theta_AT;\n+global busted.background.theta_CG:=busted.test.theta_CG;\n+global busted.background.theta_CT:=busted.test.theta_CT;\n+global busted.background.theta_GT:=busted.test.theta_GT;\n+busted.background_Q_component_1={61,61};\n+busted.background_Q_component_1[0][1]:=0.09717451507454297*t*busted.background.omega1*busted.background.theta_AC;\n+busted.background_Q_component_1[0][2]:=0.1963563685387479*t*busted.background.theta_AG;\n+busted.background_Q_component_1[0][3]:=0.1989860284705866*t*busted.background.omega1*busted.background.theta_AT;\n+busted.background_Q_component_1[0][4]:=0.1818409092376876*t*busted.background.omega1*busted.background.theta_AC;\n+busted.background_Q_component_1[0][8]:=0.1563402972714242*t*busted.background.omega1*busted.background.theta_AG;\n+busted.background_Q_component_1[0][12]:=0.2361684149931496*t*busted.background.omega1*busted.background.theta_AT;\n+busted.background_Q_component_1[0][16]:=0.1712746635706107*t*busted.background.omega1*busted.background.theta_AC;\n+busted.background_Q_component_1[0][32]:=0.2567033972679326*t*busted.background.omega1*busted.background.theta_AG;\n+busted.background_Q_component_1[1][0]:=0.5074830879161225*t*busted.background.omega1*busted.background.theta_AC;\n+busted.background_Q_component_1[1][2]:=0.1963563685387479*t*busted.background.omega1*busted.background.theta_CG;\n+busted.background_Q_component_1[1][3]:=0.1989860284705866*t*busted.background.theta_CT;\n+busted.background_Q_component_1[1][5]:=0.1818409092376876*t*busted.background.omega1*busted.background.theta_AC;\n+busted.background_Q_component_1[1][9]:=0.1563402972714242*t*busted.background.omega1*busted.background.theta_AG;\n+busted.background_Q_component_1[1][13]:=0.2361684149931496*t*busted.background.omega1*busted.background.theta_AT;\n+bu'..b'ta_CG;\n busted.test_Q_component_1[54][55]:=0.1963563685387479*t*busted.test.omega1*busted.test.theta_CG;\n busted.test_Q_component_1[54][56]:=0.1989860284705866*t*busted.test.theta_CT;\n@@ -538,7 +2205,7 @@\n busted.test_Q_component_1[56][11]:=0.3148753970510747*t*busted.test.omega1*busted.test.theta_AT;\n busted.test_Q_component_1[56][27]:=0.1712746635706107*t*busted.test.omega1*busted.test.theta_CT;\n busted.test_Q_component_1[56][43]:=0.2567033972679326*t*busted.test.omega1*busted.test.theta_GT;\n-busted.test_Q_component_1[56][49]:=0.4256503784977386*t*busted.test.omega1*busted.test.theta_AG;\n+busted.test_Q_component_1[56][49]:=0.4256503784977386*t*busted.test.theta_AG*busted.test.omega1;\n busted.test_Q_component_1[56][53]:=0.1818409092376876*t*busted.test.omega1*busted.test.theta_CG;\n busted.test_Q_component_1[56][54]:=0.09717451507454297*t*busted.test.theta_CT;\n busted.test_Q_component_1[56][55]:=0.1963563685387479*t*busted.test.omega1*busted.test.theta_GT;\n@@ -1702,29 +3369,27 @@\n Model busted.test=(\'Exp(busted.test_Q_component_1)*1*busted.test.bsrel_mixture_aux_0+Exp(busted.test_Q_component_2)*1*(1-busted.test.bsrel_mixture_aux_0)*busted.test.bsrel_mixture_aux_1+Exp(busted.test_Q_component_3)*1*(1-busted.test.bsrel_mixture_aux_0)*(1-busted.test.bsrel_mixture_aux_1)\',busted.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n TRY_NUMERIC_SEQUENCE_MATCH=0;\n ACCEPT_ROOTED_TREES=0;\n-\n-UseModel (busted.test);\n-Tree cuWdXMfP.tree_id_0=((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9);\n+Tree QCdustmY.tree_id_0=((((D_CD_83_ELI{busted.background},D_CD_83_NDK{busted.background})Node3{busted.background},D_UG_94_94UG114{busted.background})Node2{busted.background},D_CD_84_84ZR085{busted.background})Node1{busted.background},B_US_83_RF{busted.background},((B_FR_83_HXB2{busted.background},B_US_86_JRFL{busted.background})Node10{busted.background},B_US_90_WEAU160{busted.test})Node9{busted.background});\n \n-cuWdXMfP.tree_id_0.D_CD_83_ELI.t=0.1377903766097694;\n-cuWdXMfP.tree_id_0.D_CD_83_NDK.t=0.06607109645594529;\n-cuWdXMfP.tree_id_0.Node3.t=0.0890081009446355;\n-cuWdXMfP.tree_id_0.D_UG_94_94UG114.t=0.4322474154485661;\n-cuWdXMfP.tree_id_0.Node2.t=0.01436667144151429;\n-cuWdXMfP.tree_id_0.D_CD_84_84ZR085.t=0.2152052309993384;\n-cuWdXMfP.tree_id_0.Node1.t=0.1867555551194544;\n-cuWdXMfP.tree_id_0.B_US_83_RF.t=0.2093873697545922;\n-cuWdXMfP.tree_id_0.B_FR_83_HXB2.t=0.08552069057797769;\n-cuWdXMfP.tree_id_0.B_US_86_JRFL.t=0.1313117411090917;\n-cuWdXMfP.tree_id_0.Node10.t=0.01181372524396516;\n-cuWdXMfP.tree_id_0.B_US_90_WEAU160.t=0.1600546391700751;\n-cuWdXMfP.tree_id_0.Node9.t=0.03506352054252541;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n+QCdustmY.tree_id_0.D_CD_83_ELI.t=0.1370833707498818;\n+QCdustmY.tree_id_0.D_CD_83_NDK.t=0.06548157292895862;\n+QCdustmY.tree_id_0.Node3.t=0.08713663976914707;\n+QCdustmY.tree_id_0.D_UG_94_94UG114.t=0.4280587759297035;\n+QCdustmY.tree_id_0.Node2.t=0.01513176299488742;\n+QCdustmY.tree_id_0.D_CD_84_84ZR085.t=0.2130038858362291;\n+QCdustmY.tree_id_0.Node1.t=0.1846586758901705;\n+QCdustmY.tree_id_0.B_US_83_RF.t=0.2063734346567031;\n+QCdustmY.tree_id_0.B_FR_83_HXB2.t=0.08448292129897501;\n+QCdustmY.tree_id_0.B_US_86_JRFL.t=0.1299787017728399;\n+QCdustmY.tree_id_0.Node10.t=0.01154139173279806;\n+QCdustmY.tree_id_0.B_US_90_WEAU160.t=0.1759147205880889;\n+QCdustmY.tree_id_0.Node9.t=0.03592645553508322;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n \n DataSet busted.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n DataSetFilter busted.filter.default = CreateFilter(busted.codon_data,3,"0-1319","4,5,7,6,1,0,2,3","TAA,TAG,TGA");\n ASSUME_REVERSIBLE_MODELS=1;\n USE_LAST_RESULTS=0;\n-LikelihoodFunction cuWdXMfP.likelihoodFunction = (busted.filter.default,cuWdXMfP.tree_id_0);\n+LikelihoodFunction QCdustmY.likelihoodFunction = (busted.filter.default,QCdustmY.tree_id_0);\n \n END;\n\\ No newline at end of file\n' |