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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="phytab_clearcut" name="phytab clearcut" version="1.0.0">
2 <description>clearcut: Generate Neighbor Joining phylogeny. Input can be aligned fasta or phytab format.</description>
3 <requirements>
4 <requirement type="package">clearcut</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_clearcut.py -i $data -t $datatype > $clearcut_stdout 2>&amp;1
8 </command>
9 <inputs>
10 <param format="tabular" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or fasta"/>
11 <param name="datatype" type="select" format="text">
12 <label>Type of data for all partitions</label>
13 <option value="P">Protein</option>
14 <option value="D">DNA</option>
15 </param>
16 </inputs>
17 <outputs>
18 <data format="txt" name="clearcut_stdout" label="${tool.name} on ${on_string}: stdout" />
19 <data format="tabular" name="clearcut_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
20 </outputs>
21 <tests>
22 </tests>
23 <help>
24 **What it does**
25
26 This tool uses the the program Clearcut to infer a Neighbor-Joining phylogeny using the fast RNJ algorithm for a data set using uncorrected distances (p-distances).
27
28 ------
29
30 **Input**
31 The program will automatically detect possible inputs of two types
32 1. ALIGNED FASTA file for a single gene family
33
34 2. ALIGNED PHYTAB for multiple genes. See
35 http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html for description of phytab format.
36
37 ------
38
39 **Output**
40
41 A phylogenetic tree in newick format. In the Osiris package this can be visualized with a tool like TreeVector.
42
43 ------
44
45 **Additional Information**
46
47 http://bioinformatics.hungry.com/clearcut/
48
49 ------
50
51 **Citations**
52
53 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.
54
55 Current Osiris Citation is here
56
57 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
58
59 Additional Citations for this tool
60
61 Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method, J. Mol. Evol., 62, 785-792
62
63 </help>
64 </tool>
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