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