Mercurial > repos > anngomez > mrbayes
changeset 3:8741c342e8af draft
Uploaded MrBayes wrapper for dynamic commands.
author | anngomez |
---|---|
date | Thu, 08 Nov 2012 11:29:57 -0500 |
parents | 8ad0d20c9654 |
children | ad8b097df80a |
files | mrbayes.xml |
diffstat | 1 files changed, 141 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mrbayes.xml Thu Nov 08 11:29:57 2012 -0500 @@ -0,0 +1,141 @@ +<?xml version="1.0"?> +<tool id="mrbayes" name="MrBayes"> + <description>with options and commands</description> + <command> mb $command_file > $outfile</command> + <inputs> + <param name="data" type="data" format="nex" label="Nexus input file"/> + + <param name="outgroup" type="text" label="Outgroup" size="10" value="1" + help="The name or number identifying one taxon from the data." /> + <param name="model" type="select" label="Choose model"> + <sanitizer sanitize="False" /> + <option value="lset nst=6" >GRT</option> + <option value="lset nst=6; prset statefreqpr=fixed(equal)">SYM</option> + <option value="lset nst=2" >HKY</option> + <option value="lset nst=2; prset statefreqpr=fixed(equal)">K2P</option> + <option value="lset nst=1" >F81</option> + <option value="lset nst=1; prset statefreqpr=fixed(equal)">JC </option> + <option value="lset nst=mixed" >Mixed </option> + <help>Models are defined below and are only valid for nucleotide data.</help> + </param> + <param name="rates" type="select" label="Choose rates"> + <option value="equal"/> + <option value="gamma"/> + <option value="propinv"/> + <option value="invgamma"/> + <option value="adgamma"/> + </param> + <param name="ngen" type="integer" label="Number of generations" value="1000" > + <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> + </param> + <param name="nchain" type="integer" label="Number of chains" value="2" > + <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> + </param> + <param name="nrun" type="integer" label="Number of runs" value="2" > + <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> + </param> + <param name="checkfreq" type="integer" label="Checkpoint frequency" value="100000" > + <validator type="in_range" min="100" max="inf" message="Must be greater than or equal to 100"/> + <help>Frequency with which checkpoints are written. + You can continue an analysis from a checkpoint with 'mcmc append=yes'."</help> + </param> + <param name="samplefreq" type="integer" label="Sample frequency" value="500" > + <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> + <help>Frequency with which output it written to files." </help> + </param> + <param name="printfreq" type="integer" label="Print frequency" value="500" > + <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> + <help>Frequency with which output is printed to the screen.</help> + </param> + <param name="burninfrac" type="float" label="Burn-in fraction" value="0.25"> + <validator type="in_range" min="0.01" max=".50" message="Must be between 0.01 and .50"/> + <help>Fraction of samples to discard when summarizing. </help> + </param> + <param name="stoprule" type="select" label="Stop rule?" > + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + + <param name="sump" type="boolean" truevalue="sump;" falsevalue="" label="Include sump?" + help="Summarizes sampled parameter value."/> + <param name="sumt" type="boolean" truevalue="sumt;" falsevalue="" label="Include sumt?" + help="Summarizes the trees."/> + <param name="plot" type="boolean" truevalue="plot;" falsevalue="" label="Include plot?" + help="Creates an x-y graph of the parameter over the course of the chain."/> + + <!-- + </when> + </conditional> --> + + </inputs> + + <configfiles> + <configfile name="command_file"> + begin mrbayes; + set quitonerror=no; + execute $data; + outgroup $outgroup; + $model; + lset rates=$rates; + mcmcp ngen=$ngen nrun=$nrun nchain=$nchain checkfreq=$checkfreq samplefreq=$samplefreq printfreq=$printfreq stoprule=$stoprule burninfrac=$burninfrac; + mcmc; + $sump + $sumt + $plot + end; + </configfile> + </configfiles> + + <outputs> + <data name="outfile" format="txt"/> + </outputs> + + <requirements> + <requirement version="3.2.1" type="binary">mb</requirement> + </requirements> +<help> + +.. class:: warningmark + +This tool takes as input a Nexus file (.nex), described here_, that should only contain a data block, without commands. + +.. _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. + +----- + +**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** + +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 + +</help> +</tool> +