# HG changeset patch
# User nml
# Date 1450207613 18000
# Node ID 25da76152cf298c304c9bdc8724fd72bcf9bb4d2
planemo upload commit 9d6eccd6006feba67862137cb9a1d743798f71d3-dirty
diff -r 000000000000 -r 25da76152cf2 mrbayes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mrbayes.xml Tue Dec 15 14:26:53 2015 -0500
@@ -0,0 +1,199 @@
+
+
+ with options and commands
+
+ mrbayes
+
+ mb $command_file > $outfile
+## print list of avaialble variables
+#silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
+#for k,v in $searchList[2].items()
+#silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
+#end for
+#silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n")
+
+
+
+ begin mrbayes;
+ set seed=$seed;
+ set quitonerror=no;
+ execute $data;
+ outgroup $outgroup;
+ $model;
+ lset rates=$rates;
+#if str($filename) != ""
+ mcmcp filename=$filename;
+#end if#
+ mcmcp ngen=$ngen nrun=$nrun nchain=$nchain checkfreq=$checkfreq samplefreq=$samplefreq printfreq=$printfreq stoprule=$stoprule burninfrac=$burninfrac;
+#if int($ngen) >= int($checkfreq)
+ $append;
+#end if#
+ mcmc;
+ $sump
+ $sumt
+#if str($plot) == "plot"
+ plot;
+#end if#
+ end;
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+ Models are defined below and are only valid for nucleotide data.
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+ Frequency with which output it written to files."
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+ Frequency with which output is printed to the screen.
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+ Fraction of samples to discard when summarizing.
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+ Frequency with which checkpoints are written. Used for continuing analysis with append.
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+.. class:: warningmark
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+This tool takes as input a Nexus file (.nex), described here_, that should only contain a data block, without commands. If a command block exists in the file, it will be executed first, followed by the ones specified above.
+
+.. _here: http://en.wikipedia.org/wiki/Nexus_file.
+
+-----
+
+**What it does**
+
+MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
+
+See the manual_ or the `command reference`_ for more information.
+
+.. _manual: http://mrbayes.sourceforge.net/manual.php
+.. _command reference: http://mrbayes.sourceforge.net/commref_mb3.2.pdf
+
+-----
+
+**Model Definitions**
+
+Models are defined by the following MrBayes options::
+
+ GRT: lset nst=6;
+ SYM: lset nst=6; prset statefreqpr=fixed(equal);
+ HKY: lset nst=2;
+ K2P: lset nst=2; prset statefreqpr=fixed(equal);
+ F81: lset nst=1;
+ JC: lset nst=1; prset statefreqpr=fixed(equal);
+ Mixed: lset nst=mixed;
+
+Each model makes different assumptions about nucelotide substitution rates and state frequencies.
+
+The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by grouping the six rates in various combinations.
+
+-----
+
+.. class:: infomark
+
+**Tip for repetitive analyses**
+
+Note that running the same analysis on the same dataset in Galaxy will overwrite .p, .t, and .mcmc files for that dataset. This can be avoided by copying the dataset or re-uploading it, or by specifying a new filename.
+
+.. class:: infomark
+
+**Tip for using append**
+
+If you want to use the append functionality, all parameters will have to be identical to your initial analysis. The easiest way to ensure this is by using the blue "Run this job again" arrow on the dataset, and checking the additional append box. Note also that ngen will be the total number of generations, not the number of generations to add, so you should increase this value except if a run was interrupted. Selecting append while checkfreq > ngen will have no effect.
+
+-----
+
+Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/
+
+
+ @ARTICLE {huelsenbeckjpronquistf.2001,
+ author = {Huelsenbeck JP, Ronquist F.},
+ title = {MRBAYES: Bayesian inference of phylogenetic trees.},
+ journal = {Bioinformatics},
+ year = {2001},
+ volume = {17},
+ pages = {754-755},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}
+ }
+
+
diff -r 000000000000 -r 25da76152cf2 test-data/avian_ovomucoids.nex
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/avian_ovomucoids.nex Tue Dec 15 14:26:53 2015 -0500
@@ -0,0 +1,113 @@
+#NEXUS
+
+[ Data from: Laskowski, M., Jr., and W.M. Fitch. 1989. Evolution of avian ovomucoids and of birds.
+ Pp. 371-387 in B. Fernholm, K. Bremer, and H. Jornvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam. ]
+
+begin data;
+ dimensions ntax=89 nchar=88;
+ format datatype=protein missing=? gap=- matchchar=.;
+
+ matrix
+ [ 10 20 30 40 50 60 70 80 ]
+ [ . . . . . . . . ]
+ Struthio_camelus VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK
+ Rhea_americana .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S....
+ Pterocnemia_pennata .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S....
+ Casuarius_casuarius ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G....
+ Dromaius_novaehollandiae ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G....
+ Nothoprocta_cinerascens .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L..
+ Eudromia_elegans .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E
+ Pygoscelis_adeliae_f .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....
+ Pygoscelis_adeliae_y .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....
+ Spheniscus_humboldti .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S....
+ Phalacrocorax_sulcirostris .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S....
+ Anhinga_novaehollandeae .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S....
+ Nycticorax_nycticorax .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S....
+ Chauna_chavaria .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S....
+ Anseranas_semipalmata .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S....
+ Dendrocygna_arcuata .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S....
+ Dendrocygna_autumnalis .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S....
+ Dendrocygna_eytoni_d .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S....
+ Dendrocygna_eytoni_e .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S....
+ Dendrocygna_viduata .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S....
+ Coscoroba_coscoroba ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S....
+ Cygnus_atratus .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S....
+ Goose .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....
+ Anser_indicus .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....
+ Branta_canadensis .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S....
+ Cereopsis_novaehollandiae ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S....
+ Chloephaga_picta .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E
+ Duck .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E
+ Anas_platyrhynchos .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E
+ Megapodius_freycinet .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S....
+ Leipoa_ocellata IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S....
+ Ortalis_vetula ...........D.LA.EDPNL.......T-.......???????????..PN-...H..ALQEQKI.N..D..S...D.N...S....
+ Penelope_jacquacu ...........D.LA.EDP.........T-.........I..ERDKEA..PN-...H..ALQEQK..N..D..S...D.N...S....
+ Penelope_superciliaris ...........D.LVAEDP....................I..E?DKEA..PN-...H..ALQEQK..N..D..S...D.N...S....
+ Bonasa_umbellus .RF........V.LV.EDPR...T.A.....M.......I..EHD???L.AS-..E...ATME.R..N..G........N.N.S...T
+ Tympanuchus_cupido .RF........D.LVTED.H...T...............I..EHD???L.AS-..E...ATME.R..N..G........N...S....
+ Oreortyx_pictus .RF........D.LAT.E.H...T........S......I..EHDTEA..AS-..E...AT.E.R.....A........N...S....
+ Callipepla_squamata_n .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..A........N...S....
+ Callipepla_squamata_s .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..AS.......N...S....
+ Lophortyx_californicus .RF........D.LVT.E.Q...T........Y......I..EHD?EA..AS-..E...AT.E.R..N..A........N...S....
+ Colinus_virginianus .RF........D.LATEE.H...T....MS.MF......T..EHDTEA..AS-..E...AMSE.R..N..V........N...S....
+ Cyrtonyx_montezumae_l .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...AT.E.VI.N..G........N...S....
+ Cyrtonyx_montezumae_s .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...ATSE.VI.N..G........N...S....
+ Alectoris_chukar ARF..A.....D..VTED.R...T....T-.........I..EHDGETL.A--..E...AT.E.R.....G........N...S....
+ Alectoris_rufa ARF..A.....D..VTED.H...T....T-.........I..EHD???L.A--..E...AT.E.R.....G........N...S....
+ Francolinus_afer .RF..A....RD..VSEN.R...TH........SM....I..EHDREAP.AS-..E...ATME.RV.NI.G......K.N...S....
+ Francolinus_erckelii .RF..A.....D.AVSEN.R...T...N-.....M....I??EHD?EAP.AS-..E...ATME.RV.NI.G......K.N...S.K..
+ Francolinus_coqui_v .RF..A....RD..VSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....
+ Francolinus_coqui_a .RF..A....RD.AVSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S....
+ Francolinus_francolinus_a ARF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........
+ Francolinus_francolinus_v .RF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........
+ Francolinus_pondicerianus ARFS.A.....D.LVIDDPR.M.T....DS..F.M....I..EHD???LPAS-..E...DTTEER..N..G........N...S....
+ Perdix_perdix .RF........D.LVTED.Q...T...............I..EHT???L.AS-..E...ATME.R..N..G..D.....N...N....
+ Coturnix_delegorguei .RF........DE.V.DE.RF..T....NH.MF.K....I..EQDGET???S-..E...A.K..RV.N..G........N...NR...
+ Coturnix_coturnix_japonica_1 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N...........N...N....
+ Coturnix_coturnix_japonica_2 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N..G........N...N....
+ Arborophilia_torqueola .RF..S.....V..VKEDPR...T.........H..T??I?.?????????S-....M.ATME.RV.N..G........N...S....
+ Bambusicola_thoracica ARF..A.....V.LDTQE.R...T.......MS......I.IK?DKE?L.AS-..E...ETAEERI.N..G........N....N...
+ Tragopan_satyra .RF........D.LVTED.H...T...............I..GHDREAL.AS-..E...ATME.R..N..G........N...S....
+ Tragopan_temmincki .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S....
+ Lophophorus_impejanus .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S....
+ Crossoptilon_auritum .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....
+ Lophura_edwardsi .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....
+ Lophura_ignita .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S....
+ Gallus_gallus ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S....
+ Grey_jungle_fowl ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S....
+ Phasianus_colchicus .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q
+ Syrmaticus_ellioti .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S....
+ Syrmaticus_reevesii .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E
+ Chrysolophus_amherstiae .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N....
+ Polyplectron_bicalcaratum .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS....
+ Argusianus_argus_argus .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S....
+ Pavo_cristatus .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S....
+ Afropavo_congensis .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S....
+ Numida_meleagris .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S....
+ Acryllium_vulturinum .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S....
+ Meleagris_gallopavo .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S....
+ Grus_carunculatus .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....
+ Anthropoides_virgo .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S....
+ Grus_vipio IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....
+ Fulica_atra .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S....
+ Vanellus_spinosus .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E.
+ Larus_rudibundus .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E.
+ Turnix_sylvatica .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E
+ Gallirallus_australis .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S....
+ Geococcyx_californianus .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S....
+ Dacelo_novaeguineae .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S....
+ Carpococcyx_renauldi .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS....
+ Podargus_strigoides .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N....
+ ;
+end;
+
+[
+begin mrbayes;
+ [The following line will let the mcmc chain integrate
+ over the ten fixed amino-acid rate matrices. You can also fix
+ the rates to those in one of the rate matrices.]
+ prset aamodelpr=mixed;
+end;
+]
+
diff -r 000000000000 -r 25da76152cf2 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Dec 15 14:26:53 2015 -0500
@@ -0,0 +1,6 @@
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