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