| Next changeset 1:bd36a094f934 (2015-12-15) |
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Commit message:
planemo upload commit 9d6eccd6006feba67862137cb9a1d743798f71d3-dirty |
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mrbayes.xml test-data/avian_ovomucoids.nex tool_dependencies.xml |
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| 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 |
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| b'@@ -0,0 +1,199 @@\n+<?xml version="1.0"?>\n+<tool id="mrbayes" name="MrBayes" version="1.0.0">\n+ <description>with options and commands</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.6">mrbayes</requirement>\n+ </requirements>\n+ <command> mb $command_file > $outfile\n+## print list of avaialble variables\n+#silent sys.stderr.write("\\n \\n \\n ======== Cheetah template variables ========\\n")\n+#for k,v in $searchList[2].items()\n+#silent sys.stderr.write(" %s = %s\\n" % (str(k), str(v) ))\n+#end for\n+#silent sys.stderr.write("======== End of Cheetah template variables ========\\n \\n \\n")\n+ </command>\n+ <configfiles>\n+ <configfile name="command_file">\n+ begin mrbayes;\n+ set seed=$seed;\n+ set quitonerror=no;\n+ execute $data;\n+ outgroup $outgroup;\n+ $model;\n+ lset rates=$rates;\n+#if str($filename) != ""\n+ mcmcp filename=$filename;\n+#end if#\n+ mcmcp ngen=$ngen nrun=$nrun nchain=$nchain checkfreq=$checkfreq samplefreq=$samplefreq printfreq=$printfreq stoprule=$stoprule burninfrac=$burninfrac;\n+#if int($ngen) >= int($checkfreq)\n+ $append;\n+#end if#\n+ mcmc;\n+ $sump\n+ $sumt\n+#if str($plot) == "plot"\n+ plot;\n+#end if#\n+ end;\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="data" type="data" format="nex" label="Nexus input file"/>\n+\n+ <param name="filename" type="text" label="Output filename" size="10" value=""\n+ help="Output files will be named this with .p, .t, .mcmc extensions. Use to avoid overwriting files when running repeated analyses on the same dataset." />\n+\n+ <param name="ngen" type="integer" label="<hr>Number of generations" value="10000" >\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ </param>\n+ <param name="nchain" type="integer" label="Number of chains" value="2" >\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ </param>\n+ <param name="nrun" type="integer" label="Number of runs" value="2" >\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ </param>\n+\n+ <param name="outgroup" type="text" label="<hr>Outgroup" size="10" value="1"\n+ help="The name or number identifying one taxon from the data." />\n+ <param name="model" type="select" label="Choose model">\n+ <sanitizer sanitize="False" />\n+ <option value="lset nst=6" >GRT</option>\n+ <option value="lset nst=6; prset statefreqpr=fixed(equal)">SYM</option>\n+ <option value="lset nst=2" >HKY</option>\n+ <option value="lset nst=2; prset statefreqpr=fixed(equal)">K2P</option>\n+ <option value="lset nst=1" >F81</option>\n+ <option value="lset nst=1; prset statefreqpr=fixed(equal)">JC </option>\n+ <option value="lset nst=mixed" >Mixed </option>\n+ <help>Models are defined below and are only valid for nucleotide data.</help>\n+ </param>\n+ <param name="rates" type="select" label="Choose rates">\n+ <option value="equal"/>\n+ <option value="gamma"/>\n+ <option value="propinv"/>\n+ <option value="invgamma"/>\n+ <option value="adgamma"/>\n+ </param>\n+ <param name="samplefreq" type="integer" label="<hr>Sample frequency" value="500" >\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ <help>Frequency with which output it written to files." </help>\n+ </param>\n+ <param name="printfreq" type="integer" label="Print frequency" value="500" >\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ <help>Frequency with which output is printed to the screen.</help>\n+ </param>\n+ <param name="burninfrac" type="float" label="Burn-in fraction" value="0.2'..b'alysis)." />\n+ <param name="seed" type="integer" label="<hr>Seed" optional="false" value="5"\n+ help="Specify a seed with which to run the job.">\n+ <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="outfile" format="txt"/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="data" value="avian_ovomucoids.nex"/>\n+ <output name="outfile">\n+ <assert_contents>\n+ <has_text text=" 500 -- [-6144.805] (-6235.323) * [-5853.458] (-5936.317)"/>\n+ <has_text text=" 3000 -- (-4258.327) [-3872.656] * [-3961.044] (-3988.174)"/>\n+ <has_text text=" 5000 -- (-3805.933) [-3708.438] * [-3704.553] (-3727.547)"/>\n+ <has_text text=" 8000 -- [-3676.746] (-3665.247) * [-3621.851] (-3665.758)"/>\n+ <has_text text=" 10000 -- [-3639.639] (-3639.407) * [-3613.090] (-3667.495)"/>\n+ <has_text text=" 13.4 % ( 11 %) TLMultiplier(V)"/>\n+ <has_text text=" 12.4 % ( 10 %) TLMultiplier(V)"/>\n+ <has_text text=" 1 | 0.14 "/>\n+ <has_text text=" 1 | 0.19 "/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+\n+<help>\n+\n+.. class:: warningmark\n+\n+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.\n+\n+.. _here: http://en.wikipedia.org/wiki/Nexus_file.\n+\n+-----\n+\n+**What it does**\n+\n+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.\n+\n+See the manual_ or the `command reference`_ for more information.\n+\n+.. _manual: http://mrbayes.sourceforge.net/manual.php\n+.. _command reference: http://mrbayes.sourceforge.net/commref_mb3.2.pdf\n+\n+-----\n+\n+**Model Definitions**\n+\n+Models are defined by the following MrBayes options::\n+\n+ GRT: lset nst=6;\n+ SYM: lset nst=6; prset statefreqpr=fixed(equal);\n+ HKY: lset nst=2;\n+ K2P: lset nst=2; prset statefreqpr=fixed(equal);\n+ F81: lset nst=1;\n+ JC: lset nst=1; prset statefreqpr=fixed(equal);\n+ Mixed: lset nst=mixed;\n+\n+Each model makes different assumptions about nucelotide substitution rates and state frequencies.\n+\n+The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by grouping the six rates in various combinations.\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Tip for repetitive analyses**\n+\n+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.\n+\n+.. class:: infomark\n+\n+**Tip for using append**\n+\n+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.\n+\n+-----\n+\n+Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/\n+</help>\n+<citations>\n+ <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001,\n+ author = {Huelsenbeck JP, Ronquist F.},\n+ title = {MRBAYES: Bayesian inference of phylogenetic trees.},\n+ journal = {Bioinformatics},\n+ year = {2001},\n+ volume = {17},\n+ pages = {754-755},\n+ url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}\n+ }</citation>\n+</citations>\n+</tool>\n' |
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| 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 |
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| b'@@ -0,0 +1,113 @@\n+#NEXUS \r\n+\r\n+[ Data from: Laskowski, M., Jr., and W.M. Fitch. 1989. Evolution of avian ovomucoids and of birds.\r\n+ Pp. 371-387 in B. Fernholm, K. Bremer, and H. Jornvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam. ]\r\n+\r\n+begin data;\r\n+\tdimensions ntax=89 nchar=88;\r\n+\tformat datatype=protein missing=? gap=- matchchar=.;\r\n+\r\n+\tmatrix\r\n+\t[ 10 20 30 40 50 60 70 80 ]\r\n+\t[ . . . . . . . . ]\r\n+\tStruthio_camelus VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK\r\n+\tRhea_americana .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S....\r\n+\tPterocnemia_pennata .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S....\r\n+\tCasuarius_casuarius ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G....\r\n+\tDromaius_novaehollandiae ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G....\r\n+\tNothoprocta_cinerascens .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L..\r\n+\tEudromia_elegans .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E\r\n+\tPygoscelis_adeliae_f .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....\r\n+\tPygoscelis_adeliae_y .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S....\r\n+\tSpheniscus_humboldti .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S....\r\n+\tPhalacrocorax_sulcirostris .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S....\r\n+\tAnhinga_novaehollandeae .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S....\r\n+\tNycticorax_nycticorax .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S....\r\n+\tChauna_chavaria .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S....\r\n+\tAnseranas_semipalmata .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S....\r\n+\tDendrocygna_arcuata .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S....\r\n+\tDendrocygna_autumnalis .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S....\r\n+\tDendrocygna_eytoni_d .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S....\r\n+\tDendrocygna_eytoni_e .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S....\r\n+\tDendrocygna_viduata .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S....\r\n+\tCoscoroba_coscoroba ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S....\r\n+\tCygnus_atratus .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S....\r\n+\tGoose .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....\r\n+\tAnser_indicus .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S....\r\n+\tBranta_canadensis .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S....\r\n+\tCereopsis_novaehollandiae ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S....\r\n+\tChloephaga_picta .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E\r\n+\tDuck '..b'.R..N..G........N...S....\r\n+\tTragopan_temmincki .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S....\r\n+\tLophophorus_impejanus .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S....\r\n+\tCrossoptilon_auritum .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....\r\n+\tLophura_edwardsi .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S....\r\n+\tLophura_ignita .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S....\r\n+\tGallus_gallus ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S....\r\n+\tGrey_jungle_fowl ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S....\r\n+\tPhasianus_colchicus .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q\r\n+\tSyrmaticus_ellioti .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S....\r\n+\tSyrmaticus_reevesii .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E\r\n+\tChrysolophus_amherstiae .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N....\r\n+\tPolyplectron_bicalcaratum .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS....\r\n+\tArgusianus_argus_argus .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S....\r\n+\tPavo_cristatus .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S....\r\n+\tAfropavo_congensis .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S....\r\n+\tNumida_meleagris .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S....\r\n+\tAcryllium_vulturinum .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S....\r\n+\tMeleagris_gallopavo .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S....\r\n+\tGrus_carunculatus .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....\r\n+\tAnthropoides_virgo .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S....\r\n+\tGrus_vipio IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S....\r\n+\tFulica_atra .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S....\r\n+\tVanellus_spinosus .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E.\r\n+\tLarus_rudibundus .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E.\r\n+\tTurnix_sylvatica .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E\r\n+\tGallirallus_australis .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S....\r\n+\tGeococcyx_californianus .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S....\r\n+\tDacelo_novaeguineae .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S....\r\n+\tCarpococcyx_renauldi .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS....\r\n+\tPodargus_strigoides .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N....\r\n+\t;\r\n+end;\r\n+\r\n+[\r\n+begin mrbayes;\r\n+\t[The following line will let the mcmc chain integrate\r\n+\t over the ten fixed amino-acid rate matrices. You can also fix\r\n+\t the rates to those in one of the rate matrices.]\r\n+\tprset aamodelpr=mixed;\r\n+end;\r\n+]\r\n+\r\n' |
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| 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 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mrbayes" version="3.2.6"> + <repository changeset_revision="7954c50fe0a8" name="package_mrbayes_3_2_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |