comparison phylographics/TreeVector.xml @ 0:5b9a38ec4a39 draft default tip

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0:5b9a38ec4a39

<tool id="tree_vector" name="TreeVector" version="1.0">
 <description>Convert Newick tree topologies to SVG trees</description>
 <command interpreter="python">TreeVector.py
  --jarBin='~/bin/'
  --jarFile='TreeVector.jar'
  --jvmArgs='-Xmx250m'
  --input=$tree
  --svg=$output
  --shape=$shape
  --length=$length
 </command>
 <inputs>
  <param name="tree" type="data" format="tre" label="Newick tree topology"/>
  <param name="shape" type="select" label="Branch Shape">
   <option value="square">Square branches</option>
   <option value="triangle">Triangle branches</option>
  </param>  
  <param name="length" type="select" label="Branch Length">
   <option value="phylo" selected="true">Use Newick branch lengths</option>
   <option value="clad">Line up labels</option>
   <option value="simpleclad">Branch lengths all same length</option>
  </param>  
 </inputs>
 <outputs>
    <data format="svg" name="output"> </data>
 </outputs>
 <tests>
 </tests>
 <help>
**What it does**

TreeVector (Pethica et al., 2010) converts Newick format tree topologies to SVG trees.

------

**Inputs**

Newick tree topology.

------

**Outputs**

Scalable Vector Graphic (SVG) tree.

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**Citations**

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.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

TreeVector Citation

Pethica, R., Barker, G., Kovacs, T. and Gough, J. 2010. TreeVector: Scalable, Interactive, 
Phylogenetic Trees for the Web. PLoS ONE 5(1), e8934. doi: 10.1371/journal.pone.0008934
 </help>
</tool>