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comparison phylostatistics/tree_support_phyutility.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 <tool id="tree_support_phyutility" name="tree_support_phyutility"> | |
2 <description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</description> | |
3 <requirements> | |
4 <requirement type="package">phyutility</requirement> | |
5 </requirements> | |
6 <command> | |
7 java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/phyutility.jar -ts -in $treesfile -tree $besttree -out $outtree | |
8 </command> | |
9 <inputs> | |
10 <param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/> | |
11 <param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="txt" name="outtree" label="Support by ${tool.name}" /> | |
15 </outputs> | |
16 <help> | |
17 **What it does** | |
18 | |
19 Tree support RAxML calculates support values for a given tree using a set of input trees. For example, it can calculate bootstrap support for the ML tree based on a set of trees from a bootstrap analysis. | |
20 This is valuable when separating bootstrap analysis from ML analysis, and when separating bootstrap replicates in different runs, which can be concatenated and used as input for this tool. | |
21 | |
22 ------ | |
23 | |
24 **Inputs** | |
25 | |
26 1. Tree file with target tree. | |
27 | |
28 2. Set of phylogenies, branch lengths are ignored. | |
29 | |
30 ------ | |
31 | |
32 **Outputs** | |
33 | |
34 The focal tree is output with support values in Newick tree format. | |
35 | |
36 ------- | |
37 | |
38 **Additional Information** | |
39 | |
40 1. This tool Calls phyutility | |
41 | |
42 2. A similar tool is tree_support_RAxML, which works best with RAxML output | |
43 | |
44 ------- | |
45 | |
46 **Citations** | |
47 | |
48 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. | |
49 | |
50 Current Osiris Citation is here | |
51 | |
52 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
53 | |
54 Additional Citations for this tool | |
55 | |
56 Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716 | |
57 | |
58 </help> | |
59 </tool> |