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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="tree_support_raxml" name="tree_support_RAxML">
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2 <description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</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>
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7 raxmlHPC-PTHREADS-SSE3 -T 2 -f b -t $besttree -z $treesfile -m GTRCAT -n galaxy -o $Out
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8 </command>
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9 <inputs>
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10 <param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/>
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11 <param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/>
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12 <param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
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13 </inputs>
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14 <outputs>
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15 <data format="txt" name="boot_tree" label="${tool.name} Bootstrap Trees on ${on_string}" from_work_dir="RAxML_bipartitions.galaxy" />
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16 <data format="txt" name="branchlabelboots" label="${tool.name} Branchlabel bootstrap bipartitions on ${on_string}" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" />
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17 <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.galaxy" />
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18 </outputs>
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19 <help>
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20 **What it does**
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21
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22 Tree support RAxML calculates support values for a given tree using a set of input trees. For example, it can calculate bootstrap support for the ML tree based on a set of trees from a bootstrap analysis.
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23 This is valuable when separating bootstrap analysis from ML analysis, and when separating bootstrap replicates in different runs, which can be concatenated and used as input for this tool.
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24
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25 ------
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26
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27 **Inputs**
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28
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29 1. Newick format target tree, branch lengths are optional.
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30
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31 2. Set of Newick format phylogenies, branch lengths are ignored.
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32
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33 3. Optional outgroup specification. There can be no spaces in this entry.
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34
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35 ------
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36
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37 **Outputs**
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38
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39 The focal tree is output with support values in Newick tree format.
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40
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41 -------
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42
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43 **Additional Information**
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44
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45 1. This tool Calls RAxML with -f b option with -t and -z options
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46
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47 2. A similar tool is tree_support_phyutility, which works best with nexus format trees.
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48
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49 -------
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50
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51 **Citations**
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52
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53 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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54
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55 Current Osiris Citation is here
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56
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57 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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58
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59 Additional Citations for this tool
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60
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61 Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
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62 http://bioinformatics.oxfordjournals.org/content/22/21/2688.short
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63
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64 </help>
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65
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66
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67 </tool>