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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="tab2trees" name="tab2trees" version="1.0.0">
2 <description>Create PDF file of phylogeny graphics from table of tree names and Newick trees</description>
3 <command interpreter="bash">tab2trees.sh $input $output $treetype $extips $labeltax $Rfile $query $midpoint</command>
4 <inputs>
5 <param name="input" type="data" format="tabular" label="Dataset" help="First column=Tree Name. Second column=Newick phylogeny"/>
6 <param name="treetype" type="select" label="Tree Plotting Style">
7 <option value="phylogram">phylogram</option>
8 <option value="cladogram">cladogram</option>
9 <option value="fan">fan</option>
10 <option value="unrooted">unrooted</option>
11 <option value="radial">radial</option>
12 </param>
13 <param name='extips' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Exclude Tip Labels'/>
14 <param name='query' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Highlight genes with QUERY and LANDMARK1 in name using Tip Label'/>
15 <param format="tabular" name="labeltax" type="data" optional="true" label="Species to Mark File" help="Tab delimited file with 2 columns, gene, species. These will be marked on the trees." />
16 <param name='midpoint' type='boolean' checked='true' truevalue='yes' falsevalue='no' label='Midpoint Root all Trees'/>
17 </inputs>
18 <outputs>
19 <data format="txt" name="Rfile" />
20 <data format="pdf" name="output" />
21 </outputs>
22
23 <help>
24 **What it does**
25
26 Creates a "book" of multiple phylogenetic tree graphics, one per page, in pdf format.
27
28 ------
29
30 **Inputs**
31
32 tab delimited file. Column 1 is tree name column 2 is newick tree string.
33
34 ------
35
36 **Outputs**
37
38 PDF file of phylogeny graphics.
39
40 -------
41
42 **Additional Information**
43
44 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
45 osiris_phylogenetics site at bitbucket.org
46
47 -------
48
49 **Citations**
50
51 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.
52
53 Current Osiris Citation is here
54
55 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
56 </help>
57 </tool>