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