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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="SHtest" name="SHtest" version="1.0.0" force_history_refresh='True'>
2 <description> Use RAxML to calculate SHtest to compare phylogenetic tree topologies
3 </description>
4 <requirements>
5 <requirement type="package">raxml</requirement>
6 </requirements>
7 <command interpreter="perl">
8 SHtest.pl $datatype $data_file $part_file $best_tree $alt_trees
9 > $raxml_log
10 2>&amp;1
11 </command>
12 <inputs>
13 <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
14 <param name="datatype" type="select" format="text">
15 <label>Model of evolution to apply to all data partitions (-m)</label>
16 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
17 </param>
18 <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
19 <param format="txt" name="best_tree" type="data" optional="true" label="ML Tree" help="ML Tree in newick format."/>
20 <param format="txt" name="alt_trees" type="data" optional="true" label="Alt Tree(s)" help="Alternative Hypothesis Tree(s) in newick format."/>
21 </inputs>
22 <outputs>
23 <data format="txt" name="raxml_log" label="${tool.name} Screen Output on ${on_string}" />
24 <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.SH" />
25 </outputs>
26 <tests>
27 </tests>
28 <help>
29 **What it does**
30
31 SHtest performs the Shimodaira-Hasegawa statistical test to compare one tree topology to alternative tree(s). The test is implemented with RAxML.
32
33 ------
34
35 **Inputs**
36
37 #. A file in RAxML (phylipE) format. This can be made with Osiris tools phylocatenator or fasta2phylipE.
38 #. Model of evolution assumed for likelihood calculations.
39 #. An optional RAxML partition file delineates data set partitions. This can be made with Osiris tool phylocatenator.
40 #. Target phylogeny in newick format.
41 #. Alternative hypothesis phylogenetic tree(s) in newick format.
42
43 ------
44
45 **Outputs**
46
47 The output is text output from RAxML, which details the statistical value of the SH test(s).
48
49 -------
50
51 **Additional Information**
52
53 raxml Home Page:
54 http://www.exelixis-lab.org/software.html
55
56 -------
57
58 **Citations**
59
60 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
61
62 Current Osiris Citation is here
63
64 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
65
66 Additional Citations for this tool
67
68 Shimodaira H., M. Hasegawa, 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol 16:1114-1116
69
70 Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
71 http://bioinformatics.oxfordjournals.org/content/22/21/2688.short
72
73 </help>
74 </tool>