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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 <tool id="phylomatic" name="Phylomatic" version="1.0.1"> |
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2 <description>Run Phylomatic</description> |
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3 <requirements> |
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4 <requirement type="binary">Phylocom Phylomatic</requirement> |
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5 </requirements> |
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6 <command interpreter="perl">./phylomatic.pl $input1 $input2</command> |
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7 <inputs> |
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8 <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> |
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9 <param name="input2" type="data" format="txt" label="Taxonomy File" /> |
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10 </inputs> |
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11 |
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12 <outputs> |
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13 <data from_work_dir="output.txt"/> |
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14 </outputs> |
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15 |
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16 <help> |
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17 **What it does** |
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18 |
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19 Phylomatic (Webb & Donoghue, 2005) is part of the Phylocom software package (Webb et al., 2008). |
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20 Phylomatic takes your list of taxa, and first tries to match them by genus name to the megatree. Failing that, they are attached by family name. |
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21 If all the genera appear in the megatree, then that family appears resolved. If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. |
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22 Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. |
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23 |
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24 ------ |
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25 |
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26 **Inputs** |
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27 |
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28 Input 1: Phylogeny in Newick format. |
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29 Input 2: List of taxa in delimited text file. |
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30 |
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31 ------ |
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32 |
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33 **Outputs** |
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34 |
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35 Phylomatic matches input taxa to the most resolved possible position in any of a set of master |
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36 trees in the database (the 'megatrees') and returns the phylogeny in one of a variety of formats: |
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37 graphical, Newick, NEXUS, or tabular. |
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38 |
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39 ------- |
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40 |
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41 **Citations** |
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42 |
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43 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use |
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44 of this tool in a publication, please consider citing the following. |
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45 |
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46 Current Osiris Citation is here |
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47 |
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48 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html |
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49 |
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50 Additional Citations for this tool |
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51 |
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52 Phylomatic (Part of Phylocom software package) |
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53 |
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54 http://phylodiversity.net/phylomatic/html/pm2_form.html |
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55 |
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56 If you use results derived from Phylocom analyses in your publications, please cite: |
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57 |
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58 Webb, C. O., Ackerly, D. D. & Kembel, S. W. 2008. Phylocom: software for the analyses of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2089-2100. |
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59 doi: 10.1093/bioinformatics/btn358 |
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60 |
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61 Original Phylomatic citation: |
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62 |
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63 Webb, C. O. & Donoghue, M. J. 2005. Phylomatic: tree assembly for applied phylogenetics. Molecular |
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64 Ecology Resources, 5: 181-183. doi: 10.1111/j.1471-8286.2004.00829.x |
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65 </help> |
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66 </tool> |
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67 |