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planemo upload commit b361f9ed82802229277cad4433f3de57f54a06f9
author nml
date Wed, 20 Sep 2017 12:11:19 -0400
parents 2fe97192eb4b
children 905d00fb5243
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1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="mrbayes" name="MrBayes" version="1.0.1"> 2 <tool id="mrbayes" name="MrBayes" version="1.0.2">
3 <description>with options and commands</description> 3 <description>with options and commands</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2.6">mrbayes</requirement> 5 <requirement type="package" version="3.2.6">mrbayes</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/> 8 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
9 </stdio> 9 </stdio>
10 <command> mb $command_file > $outfile 10 <command>mb $command_file > $outfile
11 ## print list of avaialble variables 11 ## print list of avaialble variables
12 #silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n") 12 #silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
13 #for k,v in $searchList[2].items() 13 #for k,v in $searchList[2].items()
14 #silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) )) 14 #silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
15 #end for 15 #end for
16 #silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n") 16 #silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n")
17 </command> 17 </command>
18 <configfiles> 18 <configfiles>
19 <configfile name="command_file"> 19 <configfile name="command_file">
20 begin mrbayes; 20 begin mrbayes;
21 set Seed=$seed; 21 set Seed=$seed;
22 set Swapseed=$swapseed; 22 set Swapseed=$swapseed;
23 set quitonerror=yes; 23 set quitonerror=yes;
24 execute $data; 24 execute $data;
25 outgroup $outgroup; 25 outgroup $outgroup;
26 $model; 26 $model;
27 lset rates=$rates; 27 lset rates=$rates;
28 #if str($filename) != "" 28 #if str($filename) != ""
29 mcmcp filename=$filename; 29 mcmcp filename=$filename;
30 #end if# 30 #end if
31 mcmcp ngen=$ngen nrun=$nrun nchain=$nchain checkfreq=$checkfreq samplefreq=$samplefreq printfreq=$printfreq stoprule=$stoprule burninfrac=$burninfrac; 31 mcmcp ngen=$ngen
32 #if int($ngen) >= int($checkfreq) 32 nrun=$nrun
33 $append; 33 nchain=$nchain
34 #end if# 34 checkfreq=$checkfreq
35 mcmc; 35 samplefreq=$samplefreq
36 $sump 36 printfreq=$printfreq
37 $sumt 37 stoprule=$stoprule
38 #if str($plot) == "plot" 38 burninfrac=$burninfrac;
39 plot; 39 #if int($ngen) >= int($checkfreq)
40 #end if# 40 $append;
41 end; 41 #end if
42 </configfile> 42 mcmc;
43 </configfiles> 43 $sump
44 <inputs> 44 $sumt
45 <param name="data" type="data" format="nex" label="Nexus input file"/> 45 #if str($plot) == "plot"
46 46 plot;
47 <param name="filename" type="text" label="Output filename" size="10" value="" 47 #end if
48 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." /> 48 end;
49 49 </configfile>
50 <param name="ngen" type="integer" label="&lt;hr&gt;Number of generations" value="10000" > 50 </configfiles>
51 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 51 <inputs>
52 </param> 52 <param name="data" type="data" format="nex" label="Nexus input file"/>
53 <param name="nchain" type="integer" label="Number of chains" value="2" > 53
54 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 54 <param name="filename" type="text" label="Output filename" size="10" value=""
55 </param> 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."/>
56 <param name="nrun" type="integer" label="Number of runs" value="2" > 56
57 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 57 <param name="ngen" type="integer" label="Number of generations" value="10000">
58 </param> 58 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
59 59 </param>
60 <param name="outgroup" type="text" label="&lt;hr&gt;Outgroup" size="10" value="1" 60 <param name="nchain" type="integer" label="Number of chains" value="2">
61 help="The name or number identifying one taxon from the data." /> 61 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
62 <param name="model" type="select" label="Choose model"> 62 </param>
63 <sanitizer sanitize="False" /> 63 <param name="nrun" type="integer" label="Number of runs" value="2">
64 <option value="lset nst=6" >GRT</option> 64 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
65 <option value="lset nst=6; prset statefreqpr=fixed(equal)">SYM</option> 65 </param>
66 <option value="lset nst=2" >HKY</option> 66
67 <option value="lset nst=2; prset statefreqpr=fixed(equal)">K2P</option> 67 <param name="outgroup" type="text" label="Outgroup" size="10" value="1"
68 <option value="lset nst=1" >F81</option> 68 help="The name or number identifying one taxon from the data."/>
69 <option value="lset nst=1; prset statefreqpr=fixed(equal)">JC </option> 69 <param name="model" type="select" label="Choose model"
70 <option value="lset nst=mixed" >Mixed </option> 70 help="Models are defined below and are only valid for nucleotide data.">
71 <help>Models are defined below and are only valid for nucleotide data.</help> 71 <sanitizer sanitize="False"/>
72 </param> 72 <option value="lset nst=6">GTR</option>
73 <param name="rates" type="select" label="Choose rates"> 73 <option value="lset nst=6; prset statefreqpr=fixed(equal)">SYM</option>
74 <option value="equal"/> 74 <option value="lset nst=2">HKY85</option>
75 <option value="gamma"/> 75 <option value="lset nst=2; prset statefreqpr=fixed(equal)">K2P</option>
76 <option value="propinv"/> 76 <option value="lset nst=1">F81</option>
77 <option value="invgamma"/> 77 <option value="lset nst=1; prset statefreqpr=fixed(equal)">JC69</option>
78 <option value="adgamma"/> 78 <option value="lset nst=mixed">Mixed</option>
79 </param> 79 </param>
80 <param name="samplefreq" type="integer" label="&lt;hr&gt;Sample frequency" value="500" > 80 <param name="rates" type="select" label="Choose rates">
81 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 81 <option value="equal">(equal) No rate variation across sites</option>
82 <help>Frequency with which output it written to files." </help> 82 <option value="gamma">(gamma) Gamma-distributed rates across sites</option>
83 </param> 83 <option value="propinv">(propinv) A proportion of the sites are invariable</option>
84 <param name="printfreq" type="integer" label="Print frequency" value="500" > 84 <option value="invgamma">(invgamma) A proportion of the sites are invariable and the remaining sites are Gamma-distributed</option>
85 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 85 <option value="adgamma">(adgamma) Autocorrelated rates across sites</option>
86 <help>Frequency with which output is printed to the screen.</help> 86 </param>
87 </param> 87 <param name="samplefreq" type="integer" label="Sample frequency" value="500"
88 <param name="burninfrac" type="float" label="Burn-in fraction" value="0.25"> 88 help="Frequency with which output it written to files.">
89 <validator type="in_range" min="0.01" max=".50" message="Must be between 0.01 and .50"/> 89 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
90 <help>Fraction of samples to discard when summarizing. </help> 90 </param>
91 </param> 91 <param name="printfreq" type="integer" label="Print frequency" value="500"
92 <param name="stoprule" type="select" label="Stop rule?" > 92 help="Frequency with which output is printed to the screen.">
93 <option value="no">No</option> 93 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
94 <option value="yes">Yes</option> 94 </param>
95 </param> 95 <param name="burninfrac" type="float" label="Burn-in fraction" value="0.25"
96 <param name="sump" type="boolean" truevalue="sump;" falsevalue="" label="&lt;hr&gt;Include sump?" 96 help="Fraction of samples to discard when summarizing.">
97 help="Summarizes sampled parameter value."/> 97 <validator type="in_range" min="0.01" max=".50" message="Must be between 0.01 and .50"/>
98 <param name="sumt" type="boolean" truevalue="sumt;" falsevalue="" label="Include sumt?" 98 </param>
99 help="Summarizes the trees."/> 99 <param name="stoprule" type="select" label="Stop rule?">
100 <param name="plot" type="boolean" truevalue="plot" falsevalue="" label="Include plot?" 100 <option value="no">No</option>
101 help="Creates an x-y graph of the parameter over the course of the chain."/> 101 <option value="yes">Yes</option>
102 102 </param>
103 <param name="checkfreq" type="integer" label="&lt;hr&gt;Checkpoint frequency" value="100000" > 103 <param name="sump" type="boolean" truevalue="sump;" falsevalue="" label="Include sump?"
104 <validator type="in_range" min="100" max="inf" message="Must be greater than or equal to 100"/> 104 help="Summarizes sampled parameter value."/>
105 <help>Frequency with which checkpoints are written. Used for continuing analysis with append.</help> 105 <param name="sumt" type="boolean" truevalue="sumt;" falsevalue="" label="Include sumt?"
106 </param> 106 help="Summarizes the trees."/>
107 <param name="append" type="boolean" truevalue="mcmcp append=yes" falsevalue="mcmcp append=no" label="Append to last checkpoint?" 107 <param name="plot" type="boolean" truevalue="plot" falsevalue="" label="Include plot?"
108 help="Requires .ckp file (i.e. that number of generations > checkpoint frequency for previous analysis)." /> 108 help="Creates an x-y graph of the parameter over the course of the chain."/>
109 <param name="seed" type="integer" label="&lt;hr&gt;Seed" optional="false" value="5" 109
110 help="Specify a seed with which to run the job."> 110 <param name="checkfreq" type="integer" label="Checkpoint frequency" value="100000"
111 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 111 help="Frequency with which checkpoints are written. Used for continuing analysis with append.">
112 </param> 112 <validator type="in_range" min="100" max="2147483647" message="Must be greater than or equal to 100"/>
113 <param name="swapseed" type="integer" label="&lt;hr&gt;Swap Seed" optional="false" value="5" 113 </param>
114 help="Specify a swap seed with which to run the job."> 114 <param name="append" type="boolean" truevalue="mcmcp append=yes" falsevalue="mcmcp append=no"
115 <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/> 115 label="Append to last checkpoint?"
116 </param> 116 help="Requires .ckp file (i.e. that number of generations > checkpoint frequency for previous analysis)."/>
117 </inputs> 117 <param name="seed" type="integer" label="Seed" optional="false" value="5"
118 <outputs> 118 help="Specify a seed with which to run the job.">
119 <data name="outfile" format="txt"/> 119 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
120 </outputs> 120 </param>
121 121 <param name="swapseed" type="integer" label="Swap Seed" optional="false" value="5"
122 <tests> 122 help="Specify a swap seed with which to run the job.">
123 <test> 123 <validator type="in_range" min="1" max="2147483647" message="Must be greater than or equal to 1"/>
124 <param name="data" value="avian_ovomucoids.nex"/> 124 </param>
125 <output name="outfile"> 125 </inputs>
126 <assert_contents> 126 <outputs>
127 <has_text text=" 500 -- [-6144.805] (-6235.323) * [-5853.458] (-5936.317)"/> 127 <data name="outfile" format="txt"/>
128 <has_text text=" 3000 -- (-4258.327) [-3872.656] * [-3961.044] (-3988.174)"/> 128 </outputs>
129 <has_text text=" 5000 -- (-3805.933) [-3708.438] * [-3704.553] (-3727.547)"/> 129
130 <has_text text=" 8000 -- [-3676.746] (-3665.247) * [-3621.851] (-3665.758)"/> 130 <tests>
131 <has_text text=" 10000 -- [-3639.639] (-3639.407) * [-3613.090] (-3667.495)"/> 131 <test>
132 <has_text text=" 13.4 % ( 11 %) TLMultiplier(V)"/> 132 <param name="data" value="avian_ovomucoids.nex"/>
133 <has_text text=" 12.4 % ( 10 %) TLMultiplier(V)"/> 133 <output name="outfile">
134 <has_text text=" 1 | 0.14 "/> 134 <assert_contents>
135 <has_text text=" 1 | 0.19 "/> 135 <has_text text=" 500 -- [-6144.805] (-6235.323) * [-5853.458] (-5936.317)"/>
136 </assert_contents> 136 <has_text text=" 3000 -- (-4258.327) [-3872.656] * [-3961.044] (-3988.174)"/>
137 </output> 137 <has_text text=" 5000 -- (-3805.933) [-3708.438] * [-3704.553] (-3727.547)"/>
138 </test> 138 <has_text text=" 8000 -- [-3676.746] (-3665.247) * [-3621.851] (-3665.758)"/>
139 </tests> 139 <has_text text=" 10000 -- [-3639.639] (-3639.407) * [-3613.090] (-3667.495)"/>
140 140 <has_text text=" 13.4 % ( 11 %) TLMultiplier(V)"/>
141 <help> 141 <has_text text=" 12.4 % ( 10 %) TLMultiplier(V)"/>
142 142 <has_text text=" 1 | 0.14 "/>
143 <has_text text=" 1 | 0.19 "/>
144 </assert_contents>
145 </output>
146 </test>
147 </tests>
148
149 <help>
150 <![CDATA[
143 .. class:: warningmark 151 .. class:: warningmark
144 152
145 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. 153 This tool takes as input a Nexus file (.nex), described here_, that should only contain a data block, without
154 commands. If a command block exists in the file, it will be executed first, followed by the ones specified
155 above.
146 156
147 .. _here: http://en.wikipedia.org/wiki/Nexus_file. 157 .. _here: http://en.wikipedia.org/wiki/Nexus_file.
148 158
149 ----- 159 -----
150 160
151 **What it does** 161 **What it does**
152 162
153 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. 163 MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and
164 evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution
165 of model parameters.
154 166
155 See the manual_ or the `command reference`_ for more information. 167 See the manual_ or the `command reference`_ for more information.
156 168
157 .. _manual: http://mrbayes.sourceforge.net/manual.php 169 .. _manual: http://mrbayes.sourceforge.net/manual.php
158 .. _command reference: http://mrbayes.sourceforge.net/commref_mb3.2.pdf 170 .. _command reference: http://mrbayes.sourceforge.net/commref_mb3.2.pdf
161 173
162 **Model Definitions** 174 **Model Definitions**
163 175
164 Models are defined by the following MrBayes options:: 176 Models are defined by the following MrBayes options::
165 177
166 GRT: lset nst=6; 178 GTR: lset nst=6;
167 SYM: lset nst=6; prset statefreqpr=fixed(equal); 179 SYM: lset nst=6; prset statefreqpr=fixed(equal);
168 HKY: lset nst=2; 180 HKY85: lset nst=2;
169 K2P: lset nst=2; prset statefreqpr=fixed(equal); 181 K2P: lset nst=2; prset statefreqpr=fixed(equal);
170 F81: lset nst=1; 182 F81: lset nst=1;
171 JC: lset nst=1; prset statefreqpr=fixed(equal); 183 JC69: lset nst=1; prset statefreqpr=fixed(equal);
172 Mixed: lset nst=mixed; 184 Mixed: lset nst=mixed;
173 185
174 Each model makes different assumptions about nucelotide substitution rates and state frequencies. 186 Each model makes different assumptions about nucelotide substitution rates and state frequencies.
175 187
176 The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by grouping the six rates in various combinations. 188 The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by
189 grouping the six rates in various combinations.
177 190
178 ----- 191 -----
179 192
180 .. class:: infomark 193 .. class:: infomark
181 194
182 **Tip for repetitive analyses** 195 **Tip for repetitive analyses**
183 196
184 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. 197 Note that running the same analysis on the same dataset in Galaxy will overwrite .p, .t, and .mcmc files for
198 that dataset. This can be avoided by copying the dataset or re-uploading it, or by specifying a new filename.
185 199
186 .. class:: infomark 200 .. class:: infomark
187 201
188 **Tip for using append** 202 **Tip for using append**
189 203
190 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. 204 If you want to use the append functionality, all parameters will have to be identical to your initial analysis.
205 The easiest way to ensure this is by using the blue "Run this job again" arrow on the dataset, and checking the
206 additional append box. Note also that ngen will be the total number of generations, not the number of
207 generations to add, so you should increase this value except if a run was interrupted. Selecting append while
208 checkfreq > ngen will have no effect.
191 209
192 ----- 210 -----
193 211
194 Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/ 212 Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/
195 </help> 213 ]]>
196 <citations> 214 </help>
197 <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001, 215 <citations>
198 author = {Huelsenbeck JP, Ronquist F.}, 216 <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001,
199 title = {MRBAYES: Bayesian inference of phylogenetic trees.}, 217 author = {Huelsenbeck JP, Ronquist F.},
200 journal = {Bioinformatics}, 218 title = {MRBAYES: Bayesian inference of phylogenetic trees.},
201 year = {2001}, 219 journal = {Bioinformatics},
202 volume = {17}, 220 year = {2001},
203 pages = {754-755}, 221 volume = {17},
204 url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383} 222 pages = {754-755},
205 }</citation> 223 url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}
206 </citations> 224 }
225 </citation>
226 </citations>
207 </tool> 227 </tool>