| Previous changeset 15:81e66674859e (2020-08-21) Next changeset 17:0b58ef9e84b2 (2020-10-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80" |
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modified:
hyphy_absrel.xml test-data/absrel-out1.json |
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| diff -r 81e66674859e -r 4cc4dbca2f02 hyphy_absrel.xml --- a/hyphy_absrel.xml Fri Aug 21 15:24:17 2020 -0400 +++ b/hyphy_absrel.xml Fri Sep 18 21:10:47 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0"> +<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1"> <description>adaptive Branch Site Random Effects Likelihood</description> <macros> <import>macros.xml</import> @@ -14,6 +14,7 @@ --code '$gencodeid' --branches '$branches' --output '$absrel_output' + --multiple-hits $multiple_hits #if $log: > '$absrel_log' #end if @@ -24,6 +25,11 @@ <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> + <option value="Double">Include branch-specific rates for double nucleotide substitutions</option> + <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option> + </param> <expand macro="branches"/> </inputs> <outputs> @@ -36,6 +42,14 @@ <test> <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> + <param name="multiple_hits" value="None" /> + <param name="log" value="false"/> + <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> + </test> + <test> + <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> + <param name="multiple_hits" value="Double" /> <param name="log" value="false"/> <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/> </test> |
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| diff -r 81e66674859e -r 4cc4dbca2f02 test-data/absrel-out1.json --- a/test-data/absrel-out1.json Fri Aug 21 15:24:17 2020 -0400 +++ b/test-data/absrel-out1.json Fri Sep 18 21:10:47 2020 +0000 |
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| b'@@ -1,424 +1,253 @@\n {\n "analysis":{\n- "info":"aBSREL (Adaptive branch-site random effects likelihood)\\n uses an adaptive random effects branch-site model framework\\n to test whether each branch has evolved under positive selection,\\n using a procedure which infers an optimal number of rate categories per branch.",\n- "version":"2.0",\n- "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",\n "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\n+ "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",\n "contact":"spond@temple.edu",\n- "requirements":"in-frame codon alignment and a phylogenetic tree"\n- },\n- "input":{\n- "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",\n- "number of sequences":10,\n- "number of sites":187,\n- "partition count":1,\n- "trees":{\n- "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n- }\n- },\n- "fits":{\n- "Nucleotide GTR":{\n- "Log Likelihood":-3531.96369518556,\n- "estimated parameters":24,\n- "AIC-c":7112.577796875186,\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":0.5474707834424497,\n- "Substitution rate from nucleotide A to nucleotide G":1,\n- "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,\n- "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,\n- "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,\n- "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544\n- },\n- "display order":0\n- },\n- "Baseline MG94xREV":{\n- "Log Likelihood":-3450.669934819203,\n- "estimated parameters":46,\n- "AIC-c":6995.711784065174,\n- "Equilibrium frequencies":[\n- [0.04787662253946073],\n- [0.03913388100305117],\n- [0.04844580322128512],\n- [0.0407178971288476],\n- [0.01817959331488358],\n- [0.01485982100934833],\n- [0.01839572120297191],\n- [0.01546129971531724],\n- [0.0190238172858878],\n- [0.01554988139098808],\n- [0.01924998172104109],\n- [0.01617929156565557],\n- [0.02798385246472159],\n- [0.02287372613761008],\n- [0.02831653817605838],\n- [0.02379958245776909],\n- [0.01680670574479072],\n- [0.01373763619452979],\n- [0.01700651207463693],\n- [0.01429369239710176],\n- [0.006381800954137531],\n- [0.005216421415661322],\n- [0.006457670922102578],\n- [0.00542756570877943],\n- [0.006678159032689796],\n- [0.005458661598138652],\n- [0.00675755225029668],\n- [0.00567961101013393],\n- [0.009823507779659469],\n- [0.008029638769211124],\n- [0.009940294440024354],\n- [0.008354653231583485],\n- [0.0329096029621651],\n- [0.02689998621179963],\n- [0.03330084840219455],\n- [0.02798881284619018],\n- [0.01249635346589736],\n- [0.01021439657952951],\n- [0.01264491622176376],\n- [0.01062784315018763],\n- [0.01307665913959002],\n- [0.01068873273724336],\n- [0.0132321208528494],\n- [0.01112137894012831],\n- [0.01923563996618058],\n- [0.01572302316926395],\n- [0.01946432265285621],\n- [0.01635944157725275],\n- [0.01977100255021048],\n- '..b'\n+ [0.005501589790395056],\n+ [0.009655668202293983],\n+ [0.007888099278638223],\n+ [0.009797203904398108],\n+ [0.008223514024394991],\n+ [0.03326722643528176],\n+ [0.02717732003095303],\n+ [0.03375486749252685],\n+ [0.02833294365668738],\n+ [0.01236215156074466],\n+ [0.01009913314808799],\n+ [0.01254335971371867],\n+ [0.01052856463184265],\n+ [0.01292858539344675],\n+ [0.0105618754683007],\n+ [0.0131180965046964],\n+ [0.01101098350431497],\n+ [0.0193250328267319],\n+ [0.01578738770911659],\n+ [0.0196083049972345],\n+ [0.01645869298147252],\n+ [0.01962343746171723],\n+ [0.02045785777700414],\n+ [0.008926115885166477],\n+ [0.007292098982657142],\n+ [0.009056957588961733],\n+ [0.007602170831388156],\n+ [0.007626222986467745],\n+ [0.009471947420992787],\n+ [0.007950502328516303],\n+ [0.01395367801862353],\n+ [0.01139931439306339],\n+ [0.01415821524731906],\n+ [0.01188403168729233] \n+ ],\n+ "Log Likelihood":-3427.720059001285,\n+ "Rate Distributions":{\n+ "Per-branch delta":{\n+ "2.5%":0,\n+ "97.5%":12.07373117808175,\n+ "Mean":1.277646334033236,\n+ "Median":0.4551223038316586\n+ },\n+ "Per-branch omega":{\n+ "2.5%":0,\n+ "97.5%":2.153434974462683,\n+ "Mean":666666667.5119981,\n+ "Median":1\n+ }\n+ },\n+ "display order":1,\n+ "estimated parameters":62\n+ },\n+ "Full adaptive model":{\n+ "AIC-c":6972.859938351839,\n+ "Log Likelihood":-3415.824749853321,\n+ "Rate Distributions":{\n+ },\n+ "display order":2,\n+ "estimated parameters":68\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.857317645923,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321228205235,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,\n+ "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_input.fa",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "test results":{\n+ "P-value threshold":0.05,\n+ "positive test results":0,\n+ "tested":16\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+ "Baseline model fitting":{\n+ "order":2,\n+ "timer":17\n+ },\n+ "Complexity analysis":{\n+ "order":3,\n+ "timer":110\n+ },\n+ "Full adaptive model fitting":{\n+ "order":4,\n+ "timer":20\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":259\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":0\n+ },\n+ "Testing for selection":{\n+ "order":5,\n+ "timer":112\n+ }\n }\n }\n\\ No newline at end of file\n' |