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