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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_vector" name="TreeVector" version="1.0">
2 <description>Convert Newick tree topologies to SVG trees</description>
3 <command interpreter="python">TreeVector.py
4 --jarBin='~/bin/'
5 --jarFile='TreeVector.jar'
6 --jvmArgs='-Xmx250m'
7 --input=$tree
8 --svg=$output
9 --shape=$shape
10 --length=$length
11 </command>
12 <inputs>
13 <param name="tree" type="data" format="tre" label="Newick tree topology"/>
14 <param name="shape" type="select" label="Branch Shape">
15 <option value="square">Square branches</option>
16 <option value="triangle">Triangle branches</option>
17 </param>
18 <param name="length" type="select" label="Branch Length">
19 <option value="phylo" selected="true">Use Newick branch lengths</option>
20 <option value="clad">Line up labels</option>
21 <option value="simpleclad">Branch lengths all same length</option>
22 </param>
23 </inputs>
24 <outputs>
25 <data format="svg" name="output"> </data>
26 </outputs>
27 <tests>
28 </tests>
29 <help>
30 **What it does**
31
32 TreeVector (Pethica et al., 2010) converts Newick format tree topologies to SVG trees.
33
34 ------
35
36 **Inputs**
37
38 Newick tree topology.
39
40 ------
41
42 **Outputs**
43
44 Scalable Vector Graphic (SVG) tree.
45
46 -------
47
48 **Citations**
49
50 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
51 citing the following.
52
53 Current Osiris Citation is here
54
55 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
56
57 TreeVector Citation
58
59 Pethica, R., Barker, G., Kovacs, T. and Gough, J. 2010. TreeVector: Scalable, Interactive,
60 Phylogenetic Trees for the Web. PLoS ONE 5(1), e8934. doi: 10.1371/journal.pone.0008934
61 </help>
62 </tool>
63