| Previous changeset 8:6400b683aced (2020-03-19) Next changeset 10:4926c55123d1 (2020-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5" |
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modified:
hyphy_fel.xml macros.xml |
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added:
test-data/prime-in1.fa test-data/prime-in1.nhx test-data/prime-out1.json |
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| diff -r 6400b683aced -r 8389039f7fbc hyphy_fel.xml --- a/hyphy_fel.xml Thu Mar 19 10:17:07 2020 -0400 +++ b/hyphy_fel.xml Fri Mar 27 13:19:17 2020 -0400 |
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| @@ -17,6 +17,8 @@ --pvalue '$p_value' --output '$fel_output' > '$fel_log' + ; + @CATCH_MPIERR@ ]]></command> <inputs> <expand macro="inputs"/> @@ -42,7 +44,7 @@ <help><![CDATA[ FEL : Fixed effects likelihood ============================== - + What question does this method answer? -------------------------------------- @@ -51,9 +53,9 @@ Recommended Applications ------------------------ -The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics -(or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which -represent candidate sites subject to strong selective pressures across the entire phylogeny. +The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics +(or balancing selection), including adaptive immune escape by viruses. As such, FEL is ideally suited to identify sites under positive selection which +represent candidate sites subject to strong selective pressures across the entire phylogeny. FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. @@ -67,7 +69,7 @@ diversification or conservation. A subset of branches can be selected for testing as well, in which case an additional (nuisance) parameter will be inferred -- the non-synonymous rate on branches NOT selected for -testing. +testing. Input @@ -96,33 +98,33 @@ :: - --code Which genetic code to use + --code Which genetic code to use --branches Which branches should be tested for selection? All [default] : test all branches - - Internal : test only internal branches (suitable for + + Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data) - + Leaves: test only terminal (leaf) branches - + Unlabeled: if the Newick string is labeled using the {} notation, - test only branches without explicit labels - (see http://hyphy.org/tutorials/phylotree/) - + test only branches without explicit labels + (see http://hyphy.org/tutorials/phylotree/) + --pvalue The significance level used to determine significance - + --srv Include site-to-site synonymous rate variation? Yes [default] or No - + ]]> </help> - + <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand> |
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| diff -r 6400b683aced -r 8389039f7fbc macros.xml --- a/macros.xml Thu Mar 19 10:17:07 2020 -0400 +++ b/macros.xml Fri Mar 27 13:19:17 2020 -0400 |
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| @@ -106,7 +106,7 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.7</token> + <token name="@VERSION@">2.5.8</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> @@ -114,6 +114,13 @@ </requirements> </xml> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> + <token name="@CATCH_MPIERR@"><![CDATA[ + EC=\$? ; + if [ \$EC -ne 0 ] ; then + cat errors.log.mpinode0 >&2 ; + fi ; + exit \$EC + ]]></token> <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ export HYPHY=`which hyphy` && export HYPHY_PATH=`dirname \$HYPHY` && |
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| diff -r 6400b683aced -r 8389039f7fbc test-data/prime-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.fa Fri Mar 27 13:19:17 2020 -0400 |
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| @@ -0,0 +1,1 @@ +>HUMAN_VIETNAM_CL105_2005 ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_HEBEI_326_2005 ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG >CHICKEN_HONGKONG_915_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HUMAN_VIETNAM_3062_2004 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_HONGKONG_W355_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >MALLARD_VIETNAM_16_2003 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_CK_160_2005 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CK_HK_WF157_2003 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >SWINE_ANHUI_1_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA TCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA >HONGKONG_1_97_98 ------------------------------------------------GA CCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_SHANTOU_2216_2005 ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >PEREGRINEFALCON_HK_D0028_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HONGKONG_1_538_97 ------------------------------------------------GA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA \ No newline at end of file |
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| diff -r 6400b683aced -r 8389039f7fbc test-data/prime-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.nhx Fri Mar 27 13:19:17 2020 -0400 |
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| @@ -0,0 +1,1 @@ +((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) |
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| diff -r 6400b683aced -r 8389039f7fbc test-data/prime-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Fri Mar 27 13:19:17 2020 -0400 |
| [ |
| b'@@ -0,0 +1,391 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.123712641737602, 511.6499971244988, -5.608842688620929, -7.031699805798055, 1, 3.180962375542725, 1, -5.599238755695894, 0.7828049218517579, 1, -5.608352884924835, -2.115291881920681, 1, -5.604784076919627, -5.404956845857691, 1, -5.615111503355894, 2.462902938936584, 1, -5.607953657572869],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.849174446703908, 0.2440623951294166, -7.530855366772653, -8.547881040478554, 1, 8.833984038052169, 1, -7.53445935473729, 1.725573110573239, 1, -7.53079217870133, -0.2671292981572289, 1, -7.530980113687253, -0.4804669617756561, 1, -7.530833122267245, -0.1532486612226931, 1, -7.530868793694735],\n+ [10.63135649145974, 0, 0.7502380884715356, -7.750335490678291, -7.750335610925491, 1, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839],\n+ [0, 2.202981274414969, 0.397462976308795, -6.144243972107117, -7.361850215781605, 1, -2.763157788623757, 1, -6.146863972828472, -0.02286865932396898, 1, -6.141696705195292, 2.56489740323532, 1, -6.144140070703968, 3.673465169891661, 1, -6.162164086824393, -0.3782299185469108, 1, -6.140399389962398],\n+ [0, 6.509531966707992, 0.7279903564537584, -7.452295439546786, -8.507460649598423, 1, 6.763405786911178, 1, -7.454926555248795, 0.6678772051425989, 1, -7.451746683657063, -0.5798067642619018, 1, -7.452771449125621, -0.2211171350169704, 1, -7.452165845137638, 0.1663073214171773, 1, -7.450195387750036],\n+ [8.776439958358919, 2.284512411822656, 1.336576511778388, -9.655786100846457, -10.49206003395885, 1, 5.383393783342485, 1, -9.664210115841298, -3.158949692311737, 1, -9.655544560079083, -0.3018714845472609, 1, -9.655318226877892, 3.597509240461804, 1, -9.653746338822806, -0.0948988112495659, 1, -9.655669896512631],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 2.425089497235808, 0.5977083182449383, -7.256204136892792, -8.1869045859499, 1, 5.146566146987978, 1, -7.264970053927162, -2.513623140671756, 1, -7.255847818578761, -0.3554384584781068, 1, -7.256424962957591, 4.119925682148564, 1, -7.254165622670933, -0.1223190226259517, 1, -7.255886801654065],\n+ [6.419869332267623, 0, 0.4530400706576413, -5.863592599386944, -5.863592751403759, 1, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 2.699658477079707, 0.4801615193392039, -5.903524182207455, -6.898872136243598, 1, -0.8716130556024849, 1, -5.903538930457988, -0.4627800379305517, 1, -5.903694932983693, 3.044105631862708, 1, -5.908943461477226, -0.07628230444039112, 1, -5.903502621374115, 0.3057953308962, 1, -5.903488680659473],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, '..b' [0.0116874925496928],\n+ [0.01921743321791434],\n+ [0.00769695150511784],\n+ [0.004704463089092132],\n+ [0.005592004637968804],\n+ [0.00919478452948895],\n+ [0.03431876246786721],\n+ [0.02097601254029597],\n+ [0.02493333610872543],\n+ [0.04099722156245031],\n+ [0.006131000492593795],\n+ [0.01198292502502543],\n+ [0.004198752217504174],\n+ [0.002566324448628536],\n+ [0.003050485878513492],\n+ [0.005015832814718212],\n+ [0.001227885122343091],\n+ [0.001459537288103269],\n+ [0.002399878352343215],\n+ [0.008957344771016727],\n+ [0.00547482958980595],\n+ [0.006507708080284218],\n+ [0.01070045135026252] \n+ ],\n+ "Log Likelihood":-277.7176481414617,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.4074296362572946, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":43\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":658.4548031196325,\n+ "Equilibrium frequencies": [\n+[0.3543689320388349],\n+ [0.1790722761596548],\n+ [0.2076591154261057],\n+ [0.2588996763754045] \n+ ],\n+ "Log Likelihood":-292.5311130078037,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0,\n+ "Substitution rate from nucleotide C to nucleotide G":0,\n+ "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,\n+ "Substitution rate from nucleotide G to nucleotide T":0\n+ },\n+ "display order":0,\n+ "estimated parameters":36\n+ }\n+ },\n+ "input":{\n+ "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",\n+ "number of sequences":13,\n+ "number of sites":50,\n+ "partition count":1,\n+ "trees":{\n+ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "CHICKEN_CK_160_2005":"test",\n+ "CHICKEN_HEBEI_326_2005":"test",\n+ "CHICKEN_HONGKONG_915_97":"test",\n+ "CK_HK_WF157_2003":"test",\n+ "GOOSE_HONGKONG_W355_97":"test",\n+ "GOOSE_SHANTOU_2216_2005":"test",\n+ "HONGKONG_1_538_97":"test",\n+ "HONGKONG_1_97_98":"test",\n+ "HUMAN_VIETNAM_3062_2004":"test",\n+ "HUMAN_VIETNAM_CL105_2005":"test",\n+ "MALLARD_VIETNAM_16_2003":"test",\n+ "Node10":"test",\n+ "Node11":"test",\n+ "Node13":"test",\n+ "Node17":"test",\n+ "Node18":"test",\n+ "Node19":"test",\n+ "Node2":"test",\n+ "Node23":"test",\n+ "Node24":"test",\n+ "Node25":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node5":"test",\n+ "Node7":"test",\n+ "Node9":"test",\n+ "PEREGRINEFALCON_HK_D0028_2004":"test",\n+ "SWINE_ANHUI_1_2004":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "PRIME analysis":{\n+ "order":2,\n+ "timer":86\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":89\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |