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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_LB_pruner" name="Phytab_LB_Pruner" version="1.0">
2 <description>LB_pruner: Identify genes on very long branches.</description>
3 <requirements>
4 <requirement type="package">LB_prunerG.pl</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_LB_pruner.py -i $data -m $multiplier
8 </command>
9 <inputs>
10 <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or FASTA"/>
11 <param name="multiplier" type="float" value="4" label="Multiplier" help="Value of Multiplier, M. Branches longer than M times average are written to
12 file" >
13 </param>
14 </inputs>
15 <outputs>
16 <data format="tabular" name="LB pruner results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
17 </outputs>
18 <tests>
19 </tests>
20 <help>
21 **What it does**
22
23 LB pruner will find the average of all branch lengths in each Newick tree. Given the user-input multiplier value (M), if any branch is longer than Mx
24 the average branch length, that gene will be written to the tab-delimited output file. See outputs section for more information.
25
26 ------
27
28 **Inputs**
29
30 Sequence data file in phytab or FASTA.
31
32 Phytab description: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
33
34 Input a table as follows:::
35 name newick_tree;
36 name2 newick_tree;
37 name3 newick_tree;
38
39 Enter a value for M, the multiplier.
40
41 ------
42
43 **Outputs**
44
45 Tab delimited file listing any genes longer than Mx the average branch length for each Newick tree. If an internal branch is longer than M times the
46 average then all members of that clade are written to the out file, with 999 as the length of each branch. The third column is branch length, fourth
47 column is average branch length for each tree.
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 </help>
59 </tool>