| Previous changeset 16:af7490b6329b (2020-09-18) Next changeset 18:c32f3d3e8a92 (2020-11-19) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839" |
|
modified:
hyphy_fel.xml macros.xml test-data/slac-out1.json |
| b |
| diff -r af7490b6329b -r 2e5ab7526bd4 hyphy_fel.xml --- a/hyphy_fel.xml Fri Sep 18 21:09:33 2020 +0000 +++ b/hyphy_fel.xml Fri Oct 30 16:27:01 2020 +0000 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0"> +<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy0" profile="19.09"> <description>Fixed Effects Likelihood</description> <macros> <import>macros.xml</import> |
| b |
| diff -r af7490b6329b -r 2e5ab7526bd4 macros.xml --- a/macros.xml Fri Sep 18 21:09:33 2020 +0000 +++ b/macros.xml Fri Oct 30 16:27:01 2020 +0000 |
| [ |
| @@ -107,14 +107,14 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.17</token> + <token name="@VERSION@">2.5.21</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> - <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> + <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> <token name="@CATCH_MPIERR@"><![CDATA[ EC=\$? ; if [ \$EC -ne 0 ] ; then |
| b |
| diff -r af7490b6329b -r 2e5ab7526bd4 test-data/slac-out1.json --- a/test-data/slac-out1.json Fri Sep 18 21:09:33 2020 +0000 +++ b/test-data/slac-out1.json Fri Oct 30 16:27:01 2020 +0000 |
| [ |
| b'@@ -1,876 +1,28 @@\n {\n- "analysis":{\n- "info":"SLAC (Single Likelihood Ancestor Counting)\\n uses a maximum likelihood ancestral state reconstruction\\n and minimum path substitution counting to estimate site - level\\n dS and dN,\\n and applies a simple binomial - based test to test\\n if dS differs drom dN.\\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.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n- "version":"2.00",\n- "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",\n- "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",\n- "contact":"spond@temple.edu",\n- "requirements":"in-frame codon alignment and a phylogenetic tree"\n- },\n- "fits":{\n- "Nucleotide GTR":{\n- "Log Likelihood":-3531.963798530155,\n- "estimated parameters":24,\n- "AIC-c":7112.142458295762,\n- "Equilibrium frequencies":[\n- [0.3563279857397504],\n- [0.1837789661319073],\n- [0.2402852049910873],\n- [0.2196078431372549]\n- ],\n- "Rate Distributions":{\n- "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,\n- "Substitution rate from nucleotide A to nucleotide G":1,\n- "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n- "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n- "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n- "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n- },\n- "display order":0\n- },\n- "Global MG94xREV":{\n- "Log Likelihood":-3466.724829119623,\n- "estimated parameters":31,\n- "AIC-c":6996.52909240682,\n- "Equilibrium frequencies":[\n- [0.04785168648208005],\n- [0.03911346079312019],\n- [0.04842054060317301],\n- [0.04069665666515385],\n- [0.01817010744778396],\n- [0.01485205303123071],\n- [0.01838611113045968],\n- [0.01545321970309948],\n- [0.0190138898893362],\n- [0.01554175184587827],\n- [0.01923992433904378],\n- [0.01617083546230154],\n- [0.02796925133965702],\n- [0.02286176927319543],\n- [0.02830174586718859],\n- [0.02378714529482007],\n- [0.01687870337957799],\n- [0.01379647304851128],\n- [0.01707935503225849],\n- [0.01435491300079667],\n- [0.006409133648843443],\n- [0.005238757839512795],\n- [0.006485324528555602],\n- [0.005450807083377185],\n- [0.006706760641638982],\n- [0.005482034985409045],\n- [0.006786489669196017],\n- [0.005703931360295163],\n- [0.009865581170012171],\n- [0.008064021368173151],\n- [0.009982861811889655],\n- [0.008390428826966174],\n- [0.03287895020631181],\n- [0.02687490503171972],\n- [0.033269810543681],\n- [0.0279627207822247],\n- [0.01248470225271473],\n- [0.01020486315060615],\n- [0.01263311863778268],\n- [0.01061792547971484],\n- [0.01306446616325414],\n- [0.01067875601941112],\n- [0.01321977470017749],\n- [0.01111100011404158],\n- [0.01921770557551369],\n- [0.01570834862514353],\n- [0.01944616295744266],\n- [0.01634417558076203],\n- [0.01975257768318274],\n- [0.02055210293142003],\n- [0.009176034326710849],\n- [0.007500393094996483],\n- [0.00928511773266342],\n- [0.007803986567571961],\n- [0.00784869593340758],\n- [0.009716299514778986],\n- [0.008166387662818644],\n- [0.01412467213650941],\n- [0.01154535713247913],\n- [0.01429258425298098],\n- [0.01201267864744234]\n- ],\n- "Rate Distributions":{\n- "non-synonymous/synonymous rate ratio for *test*":[\n- [0.9952474740528205, 1]\n- ]\n- }'..b'0, 0, 0.1387249812240129, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [0.6659596192381536, 2.256767693355746, 2.5, 6, 0.2284450217013008, 3.443359136114996, 2.639155331188279, -0.367350344747201, 0.7673619164483392, 0.5300792745888832, 1.725289655759397],\n+ [1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 0.2898064092199763, 0.6666666666666667, 1, 1.725289655759397],\n+ [0.459387925258634, 2.540612074741366, 1, 2, 0.1531293084195447, 2.176809500243183, 0.7872118769661439, -0.8054285949250646, 0.9368355759475115, 0.3926328355868177, 1.725289655759397],\n+ [0.68260572574677, 2.182710391950513, 0, 5.416666666666666, 0.238230511995077, 0, 2.477393204043783, 1.327736424808056, 0.2565180128752361, 1, 1.725289655759397],\n+ [0.6209312921230391, 2.230235398735714, 1, 2, 0.2177814766543932, 1.610484143230854, 0.8967663239197839, -0.4136799968217064, 0.8783719010971742, 0.5213872231511146, 1.725289655759397],\n+ [0.7803173801516352, 2.212772241130693, 1, 5, 0.2603123363353145, 1.31349237295003, 2.302026965721967, 0.5631982273065281, 0.5099524183271413, 0.8358889331635316, 1.725289655759397],\n+ [0.5250516553536253, 2.45302813924145, 1, 6, 0.1763054355717879, 1.930849168777699, 2.513667229467984, 0.5454049260406475, 0.5662130073449929, 0.777561508830334, 1.725289655759397],\n+ [0.203181127576837, 2.790309709539656, 1, 6, 0.06787431084056803, 4.92171695238688, 2.150298936167153, -1.606349407456378, 0.9230321845151072, 0.3886057635842186, 1.725289655759397],\n+ [0.7145233834068655, 2.170085079520931, 1, 3, 0.2477020339466259, 1.399534323470248, 1.382434277951112, -0.00991140557879785, 0.7421530662286839, 0.6796980736658556, 1.725289655759397],\n+ [0.8025307113169092, 2.197469288683092, 1, 6, 0.2675102371056363, 1.246058232910557, 2.730413585709635, 0.860351389602304, 0.4023716041625731, 0.8868613698058293, 1.725289655759397],\n+ [0.886960160336796, 2.113039839663204, 1, 4, 0.295653386778932, 1.127446355223306, 1.867415205641442, 0.4068397961730323, 0.5572071130808076, 0.8144379212000086, 1.725289655759397],\n+ [0.5840734718676881, 2.415926528132312, 2.5, 5.5, 0.1946911572892293, 4.175355120340121, 2.27655929762562, -0.9098022780654729, 0.8340495404636969, 0.3957525961476541, 1.725289655759397],\n+ [0.5268550139960962, 2.205618688973626, 0, 0, 0.1928124737023075, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [1, 1.954150177116668, 1, 3, 0.3385068260057204, 0.9999999999999998, 1.535194190871489, 0.3102054133837139, 0.5833958240116991, 0.8085296778030449, 1.725289655759397],\n+ [0.7013114701420603, 2.186058834646364, 0, 2, 0.2428893408576666, 0, 0.9148884596802435, 0.530281078673453, 0.5732165501869386, 1, 1.725289655759397],\n+ [0.6103766338418385, 2.230395005807139, 1, 2, 0.2148629707938298, 1.638332702393587, 0.8967021513197104, -0.4298585739491048, 0.8813404805118064, 0.5160100083098675, 1.725289655759397],\n+ [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [1.416174943672039, 1.583825056327961, 0, 0, 0.4720583145573463, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [0.566048512190645, 2.41804757094315, 2, 3, 0.1896884337572, 3.533266066295039, 1.240670380537576, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] \n+ ]\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Ancestor sampling analysis":{\n+ "order":3,\n+ "timer":12\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":1\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":14\n+ }\n }\n }\n\\ No newline at end of file\n' |