| Previous changeset 2:f078fc88982d (2019-01-08) Next changeset 4:7782bb7bc7b7 (2019-02-12) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty |
|
modified:
hyphy_relax.xml macros.xml test-data/relax-in1.nhx |
|
added:
test-data/fade-in1.fa test-data/fade-in1.nhx test-data/fade-out1.json |
|
removed:
test-data/hyphy-in1.nhx test-data/relax-in2.nhx |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f hyphy_relax.xml --- a/hyphy_relax.xml Tue Jan 08 11:34:44 2019 -0500 +++ b/hyphy_relax.xml Mon Feb 11 20:18:43 2019 -0500 |
| [ |
| @@ -5,48 +5,36 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + <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 $gencodeid > tool_params && - echo `pwd`/relax_input.fa >> tool_params && - echo `pwd`/relax_input.nhx >> tool_params && - echo '3' && - echo '2' && - echo '$analysisType' >> tool_params && - @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' - #else: + #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 '$analysisType' > tool_params && + echo '$analysisType' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' - #end if + #else: + ln -s '$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 '2' && + echo '$analysisType' >> tool_params && + @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' + #end if ]]> </command> <inputs> - <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> - <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> - <param name="gencodeid" type="select" label="Genetic code"> - <option value="1">Universal code</option> - <option value="2">Vertebrate mitochondrial DNA code</option> - <option value="3">Yeast mitochondrial DNA code</option> - <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> - <option value="5">Invertebrate mitochondrial DNA code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> - <option value="7">Echinoderm mitochondrial DNA code</option> - <option value="8">Euplotid Nuclear code</option> - <option value="9">Alternative Yeast Nuclear code</option> - <option value="10">Ascidian mitochondrial DNA code</option> - <option value="11">Flatworm mitochondrial DNA code</option> - <option value="12">Blepharisma Nuclear code</option> - </param> + <expand macro="inputs" /> + <expand macro="gencode" /> <param name="analysisType" type="select" label="Analysis Type"> <option value="1">All</option> <option value="2">Minimal</option> @@ -58,7 +46,7 @@ </inputs> <outputs> <data name="relax_log" format="txt" /> - <data name="relax_output" format="json" from_work_dir="relax_input.fa.RELAX.json" /> + <data name="relax_output" format="hyphy_json_results" from_work_dir="relax_input.fa.RELAX.json" /> </outputs> <tests> <test> @@ -73,6 +61,6 @@ ]]> </help> <expand macro="citations"> - <citation type="doi">10.1093/molbev/msv022</citation> + <citation type="doi">10.1093/molbev/msu400</citation> </expand> </tool> |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f macros.xml --- a/macros.xml Tue Jan 08 11:34:44 2019 -0500 +++ b/macros.xml Mon Feb 11 20:18:43 2019 -0500 |
| [ |
| @@ -1,5 +1,36 @@ <?xml version="1.0"?> <macros> + <xml name="inputs"> + <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> + <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> + </xml> + <xml name="gencode"> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="1">Universal code</option> + <option value="2">Vertebrate mitochondrial DNA code</option> + <option value="3">Yeast mitochondrial DNA code</option> + <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="5">Invertebrate mitochondrial DNA code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="7">Echinoderm mitochondrial DNA code</option> + <option value="8">Euplotid Nuclear code</option> + <option value="9">Alternative Yeast Nuclear code</option> + <option value="10">Ascidian mitochondrial DNA code</option> + <option value="11">Flatworm mitochondrial DNA code</option> + <option value="12">Blepharisma Nuclear code</option> + </param> + </xml> + <xml name="branches"> + <param name="branches" type="select" label="Set of branches to test"> + <option value="1">All branches</option> + <option value="2">Internal branches</option> + <option value="3">Leaf branches</option> + <option value="4">Unlabeled branches</option> + </param> + </xml> + <xml name="version_command"> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/bti079</citation> @@ -13,9 +44,10 @@ <yield /> </requirements> </xml> - <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && export HYPHY_PATH=`dirname \$HYPHY` && -export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && -cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]> +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]> </token> -</macros> \ No newline at end of file + <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> + <token name="@HYPHYMPI_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]></token> +</macros> |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/fade-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.fa Mon Feb 11 20:18:43 2019 -0500 |
| b |
| @@ -0,0 +1,50 @@ +>Human +KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Chimp +EEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Baboon +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKIKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>RhMonkey +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIRWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKXKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTXPELNLYQDGKHVK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>Cow +----ESIVVWGALDHDLNLDIPGFPRSDIVADIKWNR--NKNKIARIKKDMPLHNEMDKY +DMFTNGTLKIKT-LMRNDSGLYEVEVYDSNGVNLLSKKFDLKIQEMLSGPEINWICTNRT +VSCKVENGSNPKLQLFLNTTRVKQDHGKLITYTWNTRWNKTFKCVASNHVDSKVSIEIAV +CPDEGLD +>Pig +-----TEVVWGIVDQDINLDIPELSKHDNVDHIRWQK--NENKIAEFKKNKETHPVKDTY +MMLPNGTLRIKD-LKRDDEGIYKVTVYATDGKHMLERKFDLPILDGVSKPVISWSCADKT +VTCEVAEGSDPKLKLYVNKSTAREGRQKVILWKWNTKWSTLFKCVASNNASEQISMVTIS +CTGQGLD +>Horse +----KNITILGALERDINLDIPAFQMSEHVEDIQWSK--GKTKIAKFKNGSMTFQKDKTY +EVLKNGTLKIKH-LERIHEGTYKVDAYDSDGKNVLEETFHLSLLEMVSKPNISWSCTNTT +LTCEVTKGTDFELKLYLNGRMIQKSPRKVIVYKRASNQIASFKCTANNTVSEESSSVVIR +CTEKGLD +>Cat +---ANDDIVWGTLGQDINLDIPDSQ-GINIDDIHWEK--GKKKVARFQISNKPKNPDEKY +NVSMNGTLKIKH-LMLEDCDTYKVVIYDKDGKNVLDKTFQLKIQEKVSTPNIDWNCINKT +LVCKVSNGTDPELKLYVNGTSIKPVSSKFSTYRFINKQKILVNCTAENKVSKESDVKMIT +CSEKGLD +>Mouse +---RDNETIWGVLGHGITLNIPNFQMTDDIDEVRWVR--RGTLVAEFKRKKPPFLISETY +EVLANGSLKIKKPMMRNDSGTYNVMVYGTNGMTRLEKDLDVRILERVSKPMIHWECPNTT +LTCAVLQGTDFELKLYQGETLLNSLPQKNMSYQW-TNLNAPFKCEAINPVSKESKMEVVN +CPEKGLS +>Rat +---RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWER--GSTLVAEFKRKMKPFLKSGAF +EILANGDLKIKN-LTRDDSGTYNVTVYSTNGTRILDKALDLRILEMVSKPMIYWECSNAT +LTCEVLEGTDVELKLYQGKEHLRSLRQKTMSYQW-TNLRAPFKCKAVNRVSQESEMEVVN +CPEKGLP |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/fade-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.nhx Mon Feb 11 20:18:43 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat: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):0.1,Mouse:0.097950); |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/fade-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-out1.json Mon Feb 11 20:18:43 2019 -0500 |
| [ |
| b'@@ -0,0 +1,4261 @@\n+{\n+ "analysis":{\n+ "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.",\n+ "version":"0.1",\n+ "citation":"TBD",\n+ "authors":"Sergei L Kosakovsky Pond",\n+ "contact":"spond@temple.edu",\n+ "requirements":"A protein alignment and a phylogenetic tree (optionally annotated with {})"\n+ },\n+ "fits":{\n+ "LG":{\n+ "Log Likelihood":-2467.815473190462,\n+ "estimated parameters":36,\n+ "AIC-c":5009.084301536408,\n+ "Rate Distributions":null,\n+ "display order":0\n+ }\n+ },\n+ "timers":{\n+ "Overall":{\n+ "timer":4940,\n+ "order":0\n+ },\n+ "Baseline Fit":{\n+ "timer":2,\n+ "order":1\n+ },\n+ "Residue A analysis":{\n+ "timer":223,\n+ "order":2\n+ },\n+ "Residue C analysis":{\n+ "timer":237,\n+ "order":3\n+ },\n+ "Residue D analysis":{\n+ "timer":219,\n+ "order":4\n+ },\n+ "Residue E analysis":{\n+ "timer":227,\n+ "order":5\n+ },\n+ "Residue F analysis":{\n+ "timer":246,\n+ "order":6\n+ },\n+ "Residue G analysis":{\n+ "timer":229,\n+ "order":7\n+ },\n+ "Residue H analysis":{\n+ "timer":333,\n+ "order":8\n+ },\n+ "Residue I analysis":{\n+ "timer":225,\n+ "order":9\n+ },\n+ "Residue K analysis":{\n+ "timer":249,\n+ "order":10\n+ },\n+ "Residue L analysis":{\n+ "timer":243,\n+ "order":11\n+ },\n+ "Residue M analysis":{\n+ "timer":239,\n+ "order":12\n+ },\n+ "Residue N analysis":{\n+ "timer":239,\n+ "order":13\n+ },\n+ "Residue P analysis":{\n+ "timer":232,\n+ "order":14\n+ },\n+ "Residue Q analysis":{\n+ "timer":233,\n+ "order":15\n+ },\n+ "Residue R analysis":{\n+ "timer":241,\n+ "order":16\n+ },\n+ "Residue S analysis":{\n+ "timer":227,\n+ "order":17\n+ },\n+ "Residue T analysis":{\n+ "timer":228,\n+ "order":18\n+ },\n+ "Residue V analysis":{\n+ "timer":236,\n+ "order":19\n+ },\n+ "Residue W analysis":{\n+ "timer":361,\n+ "order":20\n+ },\n+ "Residue Y analysis":{\n+ "timer":253,\n+ "order":21\n+ }\n+ },\n+ "input":{\n+ "file name":"/Users/ryanvelazquez/Documents/FADE/CD2_AA.fna",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"(((((Pig:0.147969,Cow:0.21343)Node4:0.085099,Horse:0.165787,Cat:0.264806)Node3:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node10:0.022733,(Human:0.004349,Chimp:0.000799)Node13:0.011873)Node9:0.101856)Node2:0.340802,Rat:0.050958)Node1:0.1,Mouse:0.09795)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Pig":"test",\n+ "Cow":"test",\n+ "Node4":"test",\n+ "Horse":"test",\n+ "Cat":"test",\n+ "Node3":"test",\n+ "RhMonkey":"test",\n+ "Baboon":"test",\n+ "Node10":"test",\n+ "Human":"test",\n+ "Chimp":"test",\n+ "Node13":"test",\n+ "Node9":"test",\n+ "Node2":"test",\n+ "Rat":"test",\n+ "Node1":"test",\n+ "Mouse":"test"\n+ }\n+ },\n+ "data partitions":{\n+ "0":{\n+ "name":"fade.filter.default",\n+ "coverage":[\n+ [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, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, '..b'4.9969794175615],\n+ [1.119100661238494, 5.801793108558826, 0.9521458856576164, 1.041389089127871, 1.026929219916273, 81.64481786080263],\n+ [1.056330043901095, 5.752962375585919, 0.9511404478663621, 1.018882211415018, 1.022829193630776, 93.11033866863323],\n+ [6.166653994189919, 5.96641384385542, 0.9487628136488599, 0.9691727453097689, 1.013506816736534, 138.0785839254452],\n+ [1.00473449821628, 5.776096442345407, 0.9523230307369015, 1.045452867183379, 1.024448297049968, 88.2012292109642],\n+ [6.951603214501662, 5.907060566996629, 0.9480298704298029, 0.9547661926885492, 1.008823963812277, 183.5341375953389],\n+ [0.6272791579648669, 5.645357813576148, 0.9504991823891995, 1.005004916524659, 1.011797297162723, 151.7372285965094],\n+ [0.5708229342619179, 5.628146900032825, 0.9501730492112415, 0.9980842629529154, 1.009917148716796, 170.3712735454202],\n+ [0.3700588702248078, 5.506111672023275, 0.9392998167466894, 0.8099217211812866, 1.001323529295577, 396.3411518078825],\n+ [0.9567722381177746, 5.732706829717117, 0.9515856362637635, 1.028732499624309, 1.020391540670269, 101.6817716881294],\n+ [0.2856854532597929, 5.449183024133389, 0.9335219429483358, 0.7349791580259242, 1.002480022689079, 335.7453701763364],\n+ [6.423598965946788, 5.95439278251374, 0.9489039767971175, 0.971994880235126, 1.013905570878258, 135.2477110030422],\n+ [0.2502394148431465, 5.416987595872403, 0.9297216596133702, 0.6924051073076462, 1.00337797394586, 300.2164451286264],\n+ [5.105016724441775, 6.014223412798681, 0.949422654856299, 0.9824995779287466, 1.017301771306348, 115.2378837918417],\n+ [0.4613616784430537, 5.597396932523158, 0.9496577869644174, 0.9873329743527605, 1.006369524238052, 222.2995049444797],\n+ [0.4452729703052817, 5.592973025353849, 0.9495820879713162, 0.9857719784809147, 1.005881553049169, 232.0881918983625],\n+ [2.569418844864073, 6.029330773966285, 0.9503479739080998, 1.001784918430241, 1.020868691945285, 99.87686729820666],\n+ [0.691797388613548, 5.662187151336211, 0.9507931926398179, 1.011322539770182, 1.012948693421484, 142.2519723257034],\n+ [0.6832164859419066, 5.657997073751089, 0.9506934421167047, 1.009170679240482, 1.012512417371037, 145.6993654882983],\n+ [4.672850848596438, 5.802302004478681, 0.9512154856689465, 1.020529908794981, 1.026711328213296, 82.17956075719567],\n+ [1.228397906666842, 5.817771819864715, 0.9521877067894924, 1.042345767016928, 1.027916087936236, 79.31151079036735],\n+ [1.556678006031996, 5.814524032270439, 0.9514507423918893, 1.025728746680229, 1.027597437073443, 80.04947274899456],\n+ [3.986555178515322, 5.949472281793122, 0.9508466999726615, 1.012480421618853, 1.025603686084447, 85.01562045867418],\n+ [0.8885542776467255, 5.731542997581703, 0.9518609011843807, 1.034914193513838, 1.020066837653431, 102.9492915238206],\n+ [1.425634972025002, 5.866806263919147, 0.9521238753762644, 1.040886264971852, 1.029668408830312, 75.49571662198383],\n+ [0.3700588702248078, 5.506111672023275, 0.9392998167466894, 0.8099217211812866, 1.001323529295577, 396.3411518078825],\n+ [1.694508786665014, 5.958932705471778, 0.9509636436149721, 1.015019841725261, 1.02610613414, 83.70410305153766],\n+ [0.74041130738418, 5.679177277588574, 0.9510426594817222, 1.016742531630482, 1.014701771238937, 129.9378952796516],\n+ [0.7491640086904585, 5.681879854018211, 0.951024322330827, 1.016342253006682, 1.015037737520547, 127.8238815540986],\n+ [0.4516850047764293, 5.549392933795774, 0.9427466555501536, 0.8618326645396361, 1.001625559096363, 378.4789043111397],\n+ [0.3758828967236633, 5.508150306080985, 0.939363793310776, 0.8108314829793968, 1.00133536768428, 395.6090151332706],\n+ [0.7589967106214373, 5.684514559084836, 0.9510607787665342, 1.017138349129698, 1.015317267807256, 126.1182390206805]\n+ ]\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/hyphy-in1.nhx --- a/test-data/hyphy-in1.nhx Tue Jan 08 11:34:44 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -((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; |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/relax-in1.nhx --- a/test-data/relax-in1.nhx Tue Jan 08 11:34:44 2019 -0500 +++ b/test-data/relax-in1.nhx Mon Feb 11 20:18:43 2019 -0500 |
| b |
| @@ -1,1 +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); \ No newline at end of file +((((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 |
| b |
| diff -r f078fc88982d -r 0648b03f1d2f test-data/relax-in2.nhx --- a/test-data/relax-in2.nhx Tue Jan 08 11:34:44 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}: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 |