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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="long_branch_finder" name="Long Branch Finder" version="1.0">
2 <description>Identifies long tips in newick trees</description>
3 <command interpreter="python">long_branch_finder.py $tabulartreelist $cutoffvalue > $output</command>
4 <inputs>
5 <param name="tabulartreelist" format="tabular" type="data" label="Tabulated list of newick trees with branch lengths" help="See format requirements and restrictions below. This input will be list of trees output from Phytab RAxML-Parsimony"/>
6 <param name="cutoffvalue" size="4" type="integer" value="1" label="Identify tips longer than ___ standard deviations of the tree's median branch length" help="Enter an integer as the cut-off."/>
7 </inputs>
8 <outputs>
9 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Long-tips list" />
10 </outputs>
11 <help>
12
13 **What it does**
14
15 Use this tool to create a list of terminal branches from one or more trees that exceed a length cut-off.
16
17 This tool calculates the statistics for the branch-length distribution in each newick tree. A terminal branch whose length falls past a specified number of standard deviations is reported in
18 the output.
19 The list output from this tool may be used to filter/prune the original PHYTAB sequence file using the tool "Prune phytab using list".
20
21 -----
22
23 **Example**
24
25 Input File (2 tab-delimited columns)::
26
27 GeneA (((Felis_catus:0.234,Canis_familiaris:0.345):0.567,Equus_monoclonius:3.98):0.564,Mus_musculus:0.456):0.0;
28 GeneB (((Felis_catus:4.123,Canis_familiaris:0.035):0.234,Equus_monoclonius:1.12):0.345,Mus_musculus:0.234):0.0;
29
30 Currently, taxon names must only include only alphanumeric characters in two fields delimted by one underscore, for example:
31
32 Genus_species
33 GENUSspecies_sample2010
34
35 If 3 standard deviations are selected as the cut-off, then the output from the example above will yield::
36
37 Equus_monoclonius geneA
38 Felis_catus geneB
39
40 Only terminal branches will be identified. (To remove entire clades subtended by long internal branches, see the tool "phytab_LB_pruner".)
41
42 -------
43
44 **Additional Information**
45
46 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org
47
48 -------
49
50 **Citations**
51
52 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.
53
54 Current Osiris Citation is here
55
56 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
57 </help>
58 </tool>