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annotate mrbayes.xml @ 3:bd2c8053e155 draft

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author nml
date Wed, 20 Sep 2017 12:11:19 -0400
parents 2fe97192eb4b
children 905d00fb5243
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1 <?xml version="1.0"?>
3
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2 <tool id="mrbayes" name="MrBayes" version="1.0.2">
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3 <description>with options and commands</description>
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4 <requirements>
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5 <requirement type="package" version="3.2.6">mrbayes</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
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9 </stdio>
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10 <command>mb $command_file > $outfile
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11 ## print list of avaialble variables
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12 #silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
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13 #for k,v in $searchList[2].items()
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14 #silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
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15 #end for
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16 #silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n")
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17 </command>
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18 <configfiles>
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19 <configfile name="command_file">
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20 begin mrbayes;
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21 set Seed=$seed;
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22 set Swapseed=$swapseed;
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23 set quitonerror=yes;
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24 execute $data;
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25 outgroup $outgroup;
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26 $model;
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27 lset rates=$rates;
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28 #if str($filename) != ""
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29 mcmcp filename=$filename;
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30 #end if
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31 mcmcp ngen=$ngen
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32 nrun=$nrun
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33 nchain=$nchain
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34 checkfreq=$checkfreq
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35 samplefreq=$samplefreq
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36 printfreq=$printfreq
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37 stoprule=$stoprule
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38 burninfrac=$burninfrac;
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39 #if int($ngen) >= int($checkfreq)
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40 $append;
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41 #end if
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42 mcmc;
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43 $sump
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44 $sumt
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45 #if str($plot) == "plot"
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46 plot;
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47 #end if
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48 end;
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49 </configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="data" type="data" format="nex" label="Nexus input file"/>
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53
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54 <param name="filename" type="text" label="Output filename" size="10" value=""
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55 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."/>
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56
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57 <param name="ngen" type="integer" label="Number of generations" value="10000">
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58 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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59 </param>
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60 <param name="nchain" type="integer" label="Number of chains" value="2">
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61 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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62 </param>
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63 <param name="nrun" type="integer" label="Number of runs" value="2">
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64 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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65 </param>
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66
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67 <param name="outgroup" type="text" label="Outgroup" size="10" value="1"
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68 help="The name or number identifying one taxon from the data."/>
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69 <param name="model" type="select" label="Choose model"
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70 help="Models are defined below and are only valid for nucleotide data.">
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71 <sanitizer sanitize="False"/>
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72 <option value="lset nst=6">GTR</option>
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73 <option value="lset nst=6; prset statefreqpr=fixed(equal)">SYM</option>
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74 <option value="lset nst=2">HKY85</option>
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75 <option value="lset nst=2; prset statefreqpr=fixed(equal)">K2P</option>
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76 <option value="lset nst=1">F81</option>
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77 <option value="lset nst=1; prset statefreqpr=fixed(equal)">JC69</option>
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78 <option value="lset nst=mixed">Mixed</option>
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79 </param>
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80 <param name="rates" type="select" label="Choose rates">
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81 <option value="equal">(equal) No rate variation across sites</option>
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82 <option value="gamma">(gamma) Gamma-distributed rates across sites</option>
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83 <option value="propinv">(propinv) A proportion of the sites are invariable</option>
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84 <option value="invgamma">(invgamma) A proportion of the sites are invariable and the remaining sites are Gamma-distributed</option>
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85 <option value="adgamma">(adgamma) Autocorrelated rates across sites</option>
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86 </param>
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87 <param name="samplefreq" type="integer" label="Sample frequency" value="500"
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88 help="Frequency with which output it written to files.">
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89 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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90 </param>
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91 <param name="printfreq" type="integer" label="Print frequency" value="500"
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92 help="Frequency with which output is printed to the screen.">
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93 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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94 </param>
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95 <param name="burninfrac" type="float" label="Burn-in fraction" value="0.25"
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96 help="Fraction of samples to discard when summarizing.">
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97 <validator type="in_range" min="0.01" max=".50" message="Must be between 0.01 and .50"/>
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98 </param>
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99 <param name="stoprule" type="select" label="Stop rule?">
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100 <option value="no">No</option>
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101 <option value="yes">Yes</option>
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102 </param>
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103 <param name="sump" type="boolean" truevalue="sump;" falsevalue="" label="Include sump?"
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104 help="Summarizes sampled parameter value."/>
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105 <param name="sumt" type="boolean" truevalue="sumt;" falsevalue="" label="Include sumt?"
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106 help="Summarizes the trees."/>
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107 <param name="plot" type="boolean" truevalue="plot" falsevalue="" label="Include plot?"
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108 help="Creates an x-y graph of the parameter over the course of the chain."/>
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109
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110 <param name="checkfreq" type="integer" label="Checkpoint frequency" value="100000"
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111 help="Frequency with which checkpoints are written. Used for continuing analysis with append.">
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112 <validator type="in_range" min="100" max="2147483647" message="Must be greater than or equal to 100"/>
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113 </param>
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114 <param name="append" type="boolean" truevalue="mcmcp append=yes" falsevalue="mcmcp append=no"
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115 label="Append to last checkpoint?"
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116 help="Requires .ckp file (i.e. that number of generations > checkpoint frequency for previous analysis)."/>
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117 <param name="seed" type="integer" label="Seed" optional="false" value="5"
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118 help="Specify a seed with which to run the job.">
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119 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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120 </param>
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121 <param name="swapseed" type="integer" label="Swap Seed" optional="false" value="5"
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122 help="Specify a swap seed with which to run the job.">
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123 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
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124 </param>
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125 </inputs>
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126 <outputs>
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127 <data name="outfile" format="txt"/>
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128 </outputs>
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129
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130 <tests>
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131 <test>
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132 <param name="data" value="avian_ovomucoids.nex"/>
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133 <output name="outfile">
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134 <assert_contents>
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135 <has_text text=" 500 -- [-6144.805] (-6235.323) * [-5853.458] (-5936.317)"/>
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136 <has_text text=" 3000 -- (-4258.327) [-3872.656] * [-3961.044] (-3988.174)"/>
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137 <has_text text=" 5000 -- (-3805.933) [-3708.438] * [-3704.553] (-3727.547)"/>
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138 <has_text text=" 8000 -- [-3676.746] (-3665.247) * [-3621.851] (-3665.758)"/>
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139 <has_text text=" 10000 -- [-3639.639] (-3639.407) * [-3613.090] (-3667.495)"/>
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140 <has_text text=" 13.4 % ( 11 %) TLMultiplier(V)"/>
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141 <has_text text=" 12.4 % ( 10 %) TLMultiplier(V)"/>
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142 <has_text text=" 1 | 0.14 "/>
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143 <has_text text=" 1 | 0.19 "/>
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144 </assert_contents>
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145 </output>
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146 </test>
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147 </tests>
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148
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149 <help>
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150 <![CDATA[
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151 .. class:: warningmark
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152
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153 This tool takes as input a Nexus file (.nex), described here_, that should only contain a data block, without
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154 commands. If a command block exists in the file, it will be executed first, followed by the ones specified
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155 above.
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156
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157 .. _here: http://en.wikipedia.org/wiki/Nexus_file.
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158
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159 -----
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160
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161 **What it does**
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162
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163 MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and
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164 evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution
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165 of model parameters.
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166
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167 See the manual_ or the `command reference`_ for more information.
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168
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169 .. _manual: http://mrbayes.sourceforge.net/manual.php
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170 .. _command reference: http://mrbayes.sourceforge.net/commref_mb3.2.pdf
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171
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172 -----
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173
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174 **Model Definitions**
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175
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176 Models are defined by the following MrBayes options::
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177
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178 GTR: lset nst=6;
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179 SYM: lset nst=6; prset statefreqpr=fixed(equal);
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180 HKY85: lset nst=2;
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181 K2P: lset nst=2; prset statefreqpr=fixed(equal);
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182 F81: lset nst=1;
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183 JC69: lset nst=1; prset statefreqpr=fixed(equal);
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184 Mixed: lset nst=mixed;
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185
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186 Each model makes different assumptions about nucelotide substitution rates and state frequencies.
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187
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188 The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by
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189 grouping the six rates in various combinations.
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190
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191 -----
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192
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193 .. class:: infomark
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194
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195 **Tip for repetitive analyses**
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196
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197 Note that running the same analysis on the same dataset in Galaxy will overwrite .p, .t, and .mcmc files for
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198 that dataset. This can be avoided by copying the dataset or re-uploading it, or by specifying a new filename.
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199
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200 .. class:: infomark
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201
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202 **Tip for using append**
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203
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204 If you want to use the append functionality, all parameters will have to be identical to your initial analysis.
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205 The easiest way to ensure this is by using the blue "Run this job again" arrow on the dataset, and checking the
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206 additional append box. Note also that ngen will be the total number of generations, not the number of
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207 generations to add, so you should increase this value except if a run was interrupted. Selecting append while
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208 checkfreq > ngen will have no effect.
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209
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210 -----
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211
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212 Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/
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213 ]]>
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214 </help>
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215 <citations>
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216 <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001,
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217 author = {Huelsenbeck JP, Ronquist F.},
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218 title = {MRBAYES: Bayesian inference of phylogenetic trees.},
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219 journal = {Bioinformatics},
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220 year = {2001},
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221 volume = {17},
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222 pages = {754-755},
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223 url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}
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224 }
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225 </citation>
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226 </citations>
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227 </tool>