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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="JModelTest" name="JModelTest 1.0" version="1.0">
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2 <description>Statistical selection of best-fit models of nucleotide substitution</description>
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3 <command interpreter="perl">
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4 #if $likelihoodInput.likelihoodStyle == "-t":
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5 jmodeltest.pl $input -t ${likelihoodInput.likelihoodPARAM} $criterion $inputType
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6 #elif $likelihoodInput.likelihoodStyle == "-u":
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7 jmodeltest.pl $input -u ${likelihoodInput.likelihoodFILE} $criterion $inputType
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8 #else:
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9 #end if#
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10 </command>
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11
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12 <inputs>
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13 <param name="inputType" type="select">
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14 <option value="fasta">FASTA</option>
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15 <option value="nex">NEXUS</option>
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16 <option value="phylip">Phylip</option>
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17 </param>
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18
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19 <param name="input" type="data" label="Input file" help="Can be: PHYLIP, FASTA or NEXUS"/>
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20
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21 <conditional name="likelihoodInput">
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22 <param name="likelihoodStyle" type="select" label="Likelihood Option" >
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23 <option value="-t">Base Tree</option>
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24 <option value="-u">User Specified Tree</option>
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25 </param>
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26
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27 <when value="-t">
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28 <param name="likelihoodPARAM" type="select" label="Likelihood options">
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29 <option value="fixed">Fixed BIONJ-JC</option>
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30 <option value="BIONJ">BIONJ</option>
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31 <option value="ML">ML Optimized</option>
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32 </param>
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33 </when>
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34
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35 <when value="-u">
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36 <param name="likelihoodFILE" type="data" format="trees" label="User specified tree file" />
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37 </when>
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38 </conditional>
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39
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40 <param name="criterion" type="select" label="Information criterion">
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41 <option value="AIC">AIC</option>
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42 <option value="BIC">BIC</option>
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43 <option value="DT">DT</option>
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44 <option value="hLRT">hLRT</option>
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45 </param>
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46
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47 </inputs>
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48
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49 <outputs>
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50 <data name="output" from_work_dir="output.txt" format="txt" />
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51 <data name="errors" from_work_dir="err_log.txt" format="txt" />
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52 </outputs>
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53 <help>
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54 **What it does**
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55
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56 "jModelTest is a new program for the statistical selection of models of nucleotide substitution based on “Phyml” (Guindon and Gascuel 2003.
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57 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.). It implements 5
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58 different selection strategies, including “hierarchical and dynamical likelihood ratio tests,” the “Akaike information criterion,” the
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59 “Bayesian information criterion,” and a “decision-theoretic performance-based” approach. This program also calculates the relative
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60 importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny."
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61
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62 (Posada, 2008; see full citation below)
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63
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64 ------
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65
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66 **Inputs**
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67
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68 Phylip, FASTA, NEXUS
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69
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70 ------
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71
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72 **Outputs**
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73
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74 Text file
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75
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76 -------
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77
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78 **Additional Information**
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79
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80 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
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81 bitbucket.org
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82
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83 -------
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84
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85 **Citations**
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86
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87 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please
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88 consider citing the following.
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89
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90 Current Osiris Citation is here
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91
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92 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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93
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94 Additional Citations for this tool
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95
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96 jModelTest: Posada, D. 2008. jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 25 (7): 1253-1256.
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97
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98 Phyml: Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood". Systematic
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99 Biology 52: 696-704.
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100 </help>
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101 </tool>