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comparison phylogenies/phytab_raxml_using_ptree.parallel.xml @ 0:5b9a38ec4a39 draft default tip

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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_raxml_using_ptree_parallel" name="RAxML using Starting trees" version="1.0">
2 <description>optimizes branch lengths on provided tree(s)</description>
3 <requirements>
4 <requirement type="package">raxml</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_raxml_using_ptree.parallel.py -i $phytabinput -e $evo -f $efile -t $startingPtreelist -T 4> $stdout 2>&amp;1
8 </command>
9 <!-- if using a queuing system, make sure number of ppn in jobrunner matches threads as set above -->
10 <inputs>
11 <param format="tabular" name="phytabinput" type="data" label="PHYTAB sequence file"/>
12 <param format="tabular" name="startingPtreelist" type="data" label="Starting trees" help="(e.g., tree list output from PHYTAB RAxML Parsimony.)"/>
13 <param name="evo" type="select" format="text">
14 <label>Model of evolution to apply to all data partitions (-m)</label>
15 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option
16 value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option
17 value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option
18 value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option
19 value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option
20 value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option
21 value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
22 </param>
23 <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab seperated file with partition name in first column, evolutionary model in the second column. Must be RAxML
24 valid model names. (optional)"/>
25
26 </inputs>
27 <outputs>
28 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
29 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
30 </outputs>
31 <tests>
32 </tests>
33 <help>
34
35 **What it does**
36
37 This tool estimates likelihood trees and branch lengths for a PHYTAB file using starting trees (e.g., parsimony trees) to accelerate tree estimation.
38
39 -------
40 **Input requirements**
41
42 1. PHYTAB sequence file
43 2. Starting tree list: two tab-delimited columns with the partition(gene) name and its newick starting tree (generated by PHYTAB RAxML-Parsimony)::
44
45 geneA (((Species_a,Species_b),Species_c),Species_d);
46 geneB ((Species_a,Species_b),(Species_c,Species_d));
47
48 See phytab description here: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
49 -------
50
51 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
52
53 -------
54
55 **Citations**
56
57 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.
58
59 Current Osiris Citation is here
60
61 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
62
63 </help>
64 </tool>
65