| Previous changeset 3:0648b03f1d2f (2019-02-11) Next changeset 5:eb2be688941a (2019-02-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty |
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modified:
hyphy_relax.xml test-data/relax-in1.nhx test-data/relax-out1.json |
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added:
test-data/hyphy-in1.nhx test-data/messages.log test-data/relax-in2.nhx |
| b |
| diff -r 0648b03f1d2f -r 7782bb7bc7b7 hyphy_relax.xml --- a/hyphy_relax.xml Mon Feb 11 20:18:43 2019 -0500 +++ b/hyphy_relax.xml Tue Feb 12 08:53:39 2019 -0500 |
| [ |
| @@ -1,20 +1,19 @@ <?xml version="1.0"?> <tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0"> - <description>Detect relaxed selection in a codon-based phylogenetic framework</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> - <command detect_errors="exit_code"> - <![CDATA[ + <description>Detect relaxed selection in a codon-based + phylogenetic framework</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ #if $treeAnnotations == 2: ln -s '$input_file' relax_input.fa && ln -s '$input_nhx' relax_input.nhx && echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && - echo '$treeAnnotations' >> tool_params && echo '3' && echo '2' && echo '$analysisType' >> tool_params && @@ -25,42 +24,38 @@ echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && - echo '$treeAnnotations' >> tool_params && echo '2' && echo '$analysisType' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' #end if - ]]> - </command> - <inputs> - <expand macro="inputs" /> - <expand macro="gencode" /> - <param name="analysisType" type="select" label="Analysis Type"> - <option value="1">All</option> - <option value="2">Minimal</option> - </param> - <param name="treeAnnotations" type="select" label="Tree Annotations"> - <option value="1">TEST only</option> - <option value="2">TEST and REFERENCE</option> - </param> - </inputs> - <outputs> - <data name="relax_log" format="txt" /> - <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" /> - </outputs> - <tests> - <test> - <param name="input_file" ftype="fasta" value="relax-in1.fa" /> - <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" /> - <output name="relax_output" file="relax-out1.json" compare="sim_size" /> - </test> - </tests> - <help> - <![CDATA[ + ]]></command> + <inputs> + <expand macro="inputs"/> + <expand macro="gencode"/> + <param name="analysisType" type="select" label="Analysis Type"> + <option value="1">All</option> + <option value="2">Minimal</option> + </param> + <param name="treeAnnotations" type="select" label="Tree Annotations"> + <option value="1">TEST only</option> + <option value="2">TEST and REFERENCE</option> + </param> + </inputs> + <outputs> + <data name="relax_log" format="txt"/> + <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json"/> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="relax-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> + <output name="relax_output" file="relax-out1.json" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ RELAX (Detect relaxed selection in a codon-based phylogenetic framework) - ]]> - </help> - <expand macro="citations"> - <citation type="doi">10.1093/molbev/msu400</citation> - </expand> + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/molbev/msu400</citation> + </expand> </tool> |
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| diff -r 0648b03f1d2f -r 7782bb7bc7b7 test-data/hyphy-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hyphy-in1.nhx Tue Feb 12 08:53:39 2019 -0500 |
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| @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
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| diff -r 0648b03f1d2f -r 7782bb7bc7b7 test-data/messages.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/messages.log Tue Feb 12 08:53:39 2019 -0500 |
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| b"@@ -0,0 +1,633 @@\n+\n+Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf\n+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf\n+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf\n+Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf\n+Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf\n+Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf\n+Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf\n+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n+Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n+Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n+Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf\n+Overwritten previously defined function:'_sortStringsAux'\n+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf\n+Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n+Already loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n+Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf\n+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n+Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n+Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n+Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n+Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf\n+Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf\n+Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf\n+Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n+Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n+Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n+Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/Templa"..b"not initialized prior to being used\n+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142\n+Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used\n+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766\n+Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used\n+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015\n+Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used\n+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678\n+Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used\n+Set GUI update interval to every 26-th LF evaluation.\n+Optimization settings:\n+\tOPTIMIZATION_METHOD = 4\n+\tOPTIMIZATION_PRECISION = 0.001\n+\tMAXIMUM_ITERATIONS_PER_VARIABLE = 5000\n+\n+Initial parameter values\n+\n+relax.test.theta_GT = 0.315401\n+relax.test.theta_CT = 0.98654\n+relax.test.theta_AC = 0.578523\n+relax.test.theta_CG = 0.469908\n+relax.test.theta_AT = 0.267066\n+relax.reference.bsrel_mixture_aux_1 = 0.818182\n+relax.reference.omega1 = 0.145496\n+relax.reference.omega2 = 0.4601\n+relax.reference.bsrel_mixture_aux_0 = 0.45\n+relax.reference.omega3 = 7.27482\n+relax.unclassified.omega3 = 1\n+relax.unclassified.bsrel_mixture_aux_1 = 0.5\n+relax.unclassified.omega2 = 1\n+relax.unclassified.omega1 = 1\n+relax.K = 1\n+relax.unclassified.bsrel_mixture_aux_0 = 0.5\n+RPGDJipv.tree_id_0.Pig.t = 1.37515\n+RPGDJipv.tree_id_0.Cow.t = 1.78195\n+RPGDJipv.tree_id_0.Node3.t = 0.71796\n+RPGDJipv.tree_id_0.Horse.t = 1.50107\n+RPGDJipv.tree_id_0.Cat.t = 1.97327\n+RPGDJipv.tree_id_0.Node2.t = 0.446186\n+RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585\n+RPGDJipv.tree_id_0.Baboon.t = 0.0125984\n+RPGDJipv.tree_id_0.Node9.t = 0.189189\n+RPGDJipv.tree_id_0.Human.t = 0\n+RPGDJipv.tree_id_0.Chimp.t = 0.0130215\n+RPGDJipv.tree_id_0.Node12.t = 0.123589\n+RPGDJipv.tree_id_0.Node8.t = 0.810855\n+RPGDJipv.tree_id_0.Node1.t = 2.05687\n+RPGDJipv.tree_id_0.Rat.t = 0.485173\n+RPGDJipv.tree_id_0.Mouse.t = 0.852285\n+Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch\n+Optimization finished in 156 loop passes.\n+19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made\n+\n+Variable 'MPI_NODE_COUNT' was not initialized prior to being used\n+Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used\n+Set GUI update interval to every 24-th LF evaluation.\n+Optimization settings:\n+\tOPTIMIZATION_METHOD = 4\n+\tOPTIMIZATION_PRECISION = 0.001\n+\tMAXIMUM_ITERATIONS_PER_VARIABLE = 5000\n+\n+Initial parameter values\n+\n+relax.test.theta_GT = 0.272534\n+relax.test.theta_CT = 0.989376\n+relax.test.theta_AC = 0.472659\n+relax.test.theta_CG = 0.409729\n+relax.test.theta_AT = 0.213063\n+relax.reference.omega2 = 0\n+relax.reference.omega3 = 1.81261\n+relax.reference.bsrel_mixture_aux_1 = 0.398417\n+relax.reference.bsrel_mixture_aux_0 = 0.26934\n+relax.reference.omega1 = 0\n+relax.unclassified.omega2 = 3.8108\n+relax.unclassified.bsrel_mixture_aux_1 = 0.965815\n+relax.unclassified.omega3 = 88.0589\n+relax.unclassified.omega1 = 0\n+relax.unclassified.bsrel_mixture_aux_0 = 0.488814\n+RPGDJipv.tree_id_0.Pig.t = 0.288673\n+RPGDJipv.tree_id_0.Cow.t = 0.415456\n+RPGDJipv.tree_id_0.Node3.t = 0.165342\n+RPGDJipv.tree_id_0.Horse.t = 0.373597\n+RPGDJipv.tree_id_0.Cat.t = 0.4862\n+RPGDJipv.tree_id_0.Node2.t = 0.071002\n+RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335\n+RPGDJipv.tree_id_0.Baboon.t = 0.00559127\n+RPGDJipv.tree_id_0.Node9.t = 0.0891892\n+RPGDJipv.tree_id_0.Human.t = 0\n+RPGDJipv.tree_id_0.Chimp.t = 0.0054891\n+RPGDJipv.tree_id_0.Node12.t = 0.0161348\n+RPGDJipv.tree_id_0.Node8.t = 0.405701\n+RPGDJipv.tree_id_0.Node1.t = 1.12055\n+RPGDJipv.tree_id_0.Rat.t = 0.217643\n+RPGDJipv.tree_id_0.Mouse.t = 0.392946\n+Optimization finished in 62 loop passes.\n+6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made\n+\n+Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used\n\\ No newline at end of file\n" |
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| diff -r 0648b03f1d2f -r 7782bb7bc7b7 test-data/relax-in1.nhx --- a/test-data/relax-in1.nhx Mon Feb 11 20:18:43 2019 -0500 +++ b/test-data/relax-in1.nhx Tue Feb 12 08:53:39 2019 -0500 |
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| @@ -1,1 +1,1 @@ -((((Pig{FG}:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108){REFERENCE}:0.022733,(Human:0.004349,Chimp:0.000799){REFERENCE}:0.011873){REFERENCE}:0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file +((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file |
| b |
| diff -r 0648b03f1d2f -r 7782bb7bc7b7 test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Tue Feb 12 08:53:39 2019 -0500 |
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| @@ -0,0 +1,1 @@ +((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795) |
| b |
| diff -r 0648b03f1d2f -r 7782bb7bc7b7 test-data/relax-out1.json --- a/test-data/relax-out1.json Mon Feb 11 20:18:43 2019 -0500 +++ b/test-data/relax-out1.json Tue Feb 12 08:53:39 2019 -0500 |
| [ |
| b'@@ -8,7 +8,7 @@\n "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"\n },\n "input":{\n- "file name":"/Users/ryanvelazquez/Documents/misc/galaxy items/tools-iuc/tools/hyphy/test-data/relax-in1.fa",\n+ "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa",\n "number of sequences":10,\n "number of sites":187,\n "partition count":1,\n@@ -38,9 +38,9 @@\n "display order":0\n },\n "MG94xREV with separate rates for branch sets":{\n- "Log Likelihood":-3458.097783887836,\n- "estimated parameters":33,\n- "AIC-c":6983.417789997894,\n+ "Log Likelihood":-3460.931903299487,\n+ "estimated parameters":32,\n+ "AIC-c":6987.013507197776,\n "Equilibrium frequencies":[\n [0.04785168648208005],\n [0.03911346079312019],\n@@ -106,131 +106,194 @@\n ],\n "Rate Distributions":{\n "non-synonymous/synonymous rate ratio for *Reference*":[\n- [0.5998337130511077, 1]\n+ [1.617765969026557, 1]\n ],\n "non-synonymous/synonymous rate ratio for *Test*":[\n- [1.554836363231672, 1]\n- ],\n- "non-synonymous/synonymous rate ratio for *Unclassified*":[\n- [1.323008542237338, 1]\n+ [0.7687683974183303, 1]\n ]\n },\n "display order":1\n },\n+ "General descriptive":{\n+ "Log Likelihood":-3420.975369746331,\n+ "estimated parameters":51,\n+ "AIC-c":6946.868231241836,\n+ "Rate Distributions":{\n+ "Shared":{\n+ "0":{\n+ "omega":1e-08,\n+ "proportion":0.2345034364701236\n+ },\n+ "1":{\n+ "omega":1e-08,\n+ "proportion":0.3180344596999608\n+ },\n+ "2":{\n+ "omega":6.64943557055033,\n+ "proportion":0.4474621038299156\n+ }\n+ }\n+ },\n+ "display order":4\n+ },\n "RELAX alternative":{\n- "Log Likelihood":-3427.641466344699,\n- "estimated parameters":41,\n- "AIC-c":6939.166958947604,\n+ "Log Likelihood":-3429.125323833579,\n+ "estimated parameters":36,\n+ "AIC-c":6931.704002822642,\n "Rate Distributions":{\n "Test":{\n "0":{\n "omega":0,\n- "proportion":0.2911071539848986\n+ "proportion":0.1993913071931658\n },\n "1":{\n "omega":0,\n- "proportion":0.2693397808592169\n+ "proportion":0.3360341729181165\n },\n "2":{\n- "omega":5.424306690747749,\n- "proportion":0.4395530651558845\n+ "omega":2.153056268947235,\n+ "proportion":0.4645745198887177\n }\n },\n "Reference":{\n "0":{\n "omega":0,\n- "proportion":0.2911071539848986\n+ "proportion":0.1993913071931658\n },\n "1":{\n "omega":0,\n- "proportion":0.2693397808592169\n+ "proportion":0.3360341729181165\n },\n "2":{\n- "omega":1.812613591933097,\n- "proportion":0.4395530651558845\n+ "omega":6.166712663934246,\n+ "proportion":0.4645745198887177\n }\n }\n },\n "display order":2\n },\n "RELAX null":{\n- "Log Likelihood":-3434.619492705835,\n- "estimated parameters":40,\n- "AIC-c":6951.032315100023,\n+ "Log Likelihood":-3437.187429488768,\n+ "estimated parameters":35,\n+ "AIC-c":6945.748904779063,\n "Rate Distributions":{\n "Test":{\n "0":{\n- "omega":0.1293481638748959,\n- "proportion":0.4017058334895309\n+ "omega":0.1177689533662908,\n+ "proportion":0.4926494715348529\n },\n "1":{\n- "omega":0.2021540589664449,\n- "proportion":0.2729236995381347\n+ "omega":0.3195682613972807,\n+ "proportion":0.1517366025099117\n },\n '..b'ith separate rates for branch sets":0.2884041028198522,\n- "RELAX alternative":0.3730383578090298,\n- "RELAX null":0.451812176248499\n+ "MG94xREV with separate rates for branch sets":0.286127507474972,\n+ "General descriptive":0.3532216661512288,\n+ "k (general descriptive)":0.2199586786715634,\n+ "RELAX alternative":0.3833004811985787,\n+ "RELAX null":0.4576044234710181,\n+ "RELAX partitioned descriptive":0.4360897576025625\n },\n "Node12":{\n "Nucleotide GTR":0.01783222754921504,\n- "MG94xREV with separate rates for branch sets":0.01732908050208956,\n- "RELAX alternative":0.01753088629189957,\n- "RELAX null":0.01907243110988959\n+ "MG94xREV with separate rates for branch sets":0.01799298835381691,\n+ "General descriptive":0.01771170858901891,\n+ "k (general descriptive)":0.1560499010177516,\n+ "RELAX alternative":0.01833338832069913,\n+ "RELAX null":0.01828012634520382,\n+ "RELAX partitioned descriptive":0.01877701767421286\n },\n "Node2":{\n "Nucleotide GTR":0.06619118337434968,\n- "MG94xREV with separate rates for branch sets":0.06256202484222494,\n- "RELAX alternative":0.0560159229945103,\n- "RELAX null":0.05930942174393248\n+ "MG94xREV with separate rates for branch sets":0.06192085035608558,\n+ "General descriptive":0.05843310574046084,\n+ "k (general descriptive)":0.2816499194095207,\n+ "RELAX alternative":0.05469841675490748,\n+ "RELAX null":0.06219694236954142,\n+ "RELAX partitioned descriptive":0.06011281230238084\n },\n "Node3":{\n "Nucleotide GTR":0.09883746945145887,\n- "MG94xREV with separate rates for branch sets":0.1006688620480881,\n- "RELAX alternative":0.1304440727067901,\n- "RELAX null":0.12356636531614\n+ "MG94xREV with separate rates for branch sets":0.09744342239018626,\n+ "General descriptive":0.1340338084149808,\n+ "k (general descriptive)":0.8358980179450297,\n+ "RELAX alternative":0.1164056814082033,\n+ "RELAX null":0.1282588343299434,\n+ "RELAX partitioned descriptive":0.1194563668460339\n },\n "Node8":{\n "Nucleotide GTR":0.106110061225871,\n- "MG94xREV with separate rates for branch sets":0.1136940853020744,\n- "RELAX alternative":0.1350606162092146,\n- "RELAX null":0.1366048365485918\n+ "MG94xREV with separate rates for branch sets":0.1090208137603471,\n+ "General descriptive":0.1401594332730181,\n+ "k (general descriptive)":0.9135621448569878,\n+ "RELAX alternative":0.1275155316795084,\n+ "RELAX null":0.1346842719904758,\n+ "RELAX partitioned descriptive":0.1358683972849559\n },\n "Node9":{\n "Nucleotide GTR":0.02567391471029082,\n- "MG94xREV with separate rates for branch sets":0.02652712807205039,\n- "RELAX alternative":0.02969171453244129,\n- "RELAX null":0.02893959719634103\n+ "MG94xREV with separate rates for branch sets":0.02582385148170195,\n+ "General descriptive":0.02665352479510937,\n+ "k (general descriptive)":0.1089752436854629,\n+ "RELAX alternative":0.02681134359856903,\n+ "RELAX null":0.02759760291393045,\n+ "RELAX partitioned descriptive":0.02746061131173372\n }\n },\n "attributes":{\n@@ -363,6 +474,14 @@\n "attribute type":"branch length",\n "display order":1\n },\n+ "General descriptive":{\n+ "attribute type":"branch length",\n+ "display order":4\n+ },\n+ "k (general descriptive)":{\n+ "attribute type":"branch label",\n+ "display order":4\n+ },\n "RELAX alternative":{\n "attribute type":"branch length",\n "display order":2\n@@ -370,6 +489,10 @@\n "RELAX null":{\n "attribute type":"branch length",\n "display order":3\n+ },\n+ "RELAX partitioned descriptive":{\n+ "attribute type":"branch length",\n+ "display order":5\n }\n }\n }\n' |