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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="raxml_pars" name="raxml_pars" version="1.0.0" force_history_refresh='True'>
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2 <description> Use RAxML to calculate a phylogeny with Parsimony </description>
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3 <requirements>
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4 <requirement type="package">raxml</requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 raxml_pars.pl $datatype $data_file $part_file
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8 $seed $Out > $raxml_log
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9 2>&amp;1
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10 </command>
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11 <inputs>
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12 <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
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13 <param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
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14 <param name="datatype" type="select" label="Data Type" help="If you have multiple, mixed data types, specify them in a partition file ">
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15 <option value="PROTGAMMAWAG">PROTEIN</option>
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16 <option value="GTRGAMMA">DNA</option>
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17 <option value="BINGAMMA">BINARY</option>
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18 <option value="MULTIGAMMA">Multistate Morphology</option>
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19 </param>
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20 <param name="seed" type="integer" value="1234567" label="Random Number Seed for search"/>
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21 <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
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22 <param name="Run" type="text" label="Run Name" help="For Galaxy History"/>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="raxml_log" label="$Run: ${tool.name} Screen Output on ${on_string}" />
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26 <data format="txt" name="raxml_info" label="$Run: ${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.parsimony" />
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27 <data format="txt" name="best_trees" label="$Run: ${tool.name} MP Tree ${on_string}" from_work_dir="RAxML_parsimonyTree.parsimony" />
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28 </outputs>
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29 <tests>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 RAxML_pars estimates phylogenetic trees, in this case calling a Parsimony algorithm.
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35
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36 ------
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37
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38 **Inputs**
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39
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40 Input file is a RAxML compatible text file. This can be generated by Osiris tools from an aligned fasta file with fasta2phylipE or from a PHYTAB format file with phylocatenator.
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41
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42 ------
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43
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44 **Outputs**
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45
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46 RAxML writes the resulting tree file in newick text format, which can be viewed in Osiris with TreeVector (of the mothur package).
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47
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48 -------
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49
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50 **Additional Information**
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51
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52 raxml Home Page.
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53 http://www.exelixis-lab.org/software.html
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54
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55 -------
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56
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57 **Citations**
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58
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59 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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60
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61 Current Osiris Citation is here
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62
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63 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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64
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65 Additional Citations for this tool
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66
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67 Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
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68 http://bioinformatics.oxfordjournals.org/content/22/21/2688.short
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69
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70 </help>
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71 </tool>
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72
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73