Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison phylostatistics/tree_support_raxml.xml @ 0:5b9a38ec4a39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5b9a38ec4a39
1 <tool id="tree_support_raxml" name="tree_support_RAxML">
2 <description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</description>
3 <requirements>
4 <requirement type="package">raxml</requirement>
5 </requirements>
6 <command>
7 raxmlHPC-PTHREADS-SSE3 -T 2 -f b -t $besttree -z $treesfile -m GTRCAT -n galaxy -o $Out
8 </command>
9 <inputs>
10 <param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/>
11 <param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/>
12 <param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
13 </inputs>
14 <outputs>
15 <data format="txt" name="boot_tree" label="${tool.name} Bootstrap Trees on ${on_string}" from_work_dir="RAxML_bipartitions.galaxy" />
16 <data format="txt" name="branchlabelboots" label="${tool.name} Branchlabel bootstrap bipartitions on ${on_string}" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" />
17 <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.galaxy" />
18 </outputs>
19 <help>
20 **What it does**
21
22 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.
23 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.
24
25 ------
26
27 **Inputs**
28
29 1. Newick format target tree, branch lengths are optional.
30
31 2. Set of Newick format phylogenies, branch lengths are ignored.
32
33 3. Optional outgroup specification. There can be no spaces in this entry.
34
35 ------
36
37 **Outputs**
38
39 The focal tree is output with support values in Newick tree format.
40
41 -------
42
43 **Additional Information**
44
45 1. This tool Calls RAxML with -f b option with -t and -z options
46
47 2. A similar tool is tree_support_phyutility, which works best with nexus format trees.
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 Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
62 http://bioinformatics.oxfordjournals.org/content/22/21/2688.short
63
64 </help>
65
66
67 </tool>