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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" name="Phytab RAxML" version="1.1">
2 <description> for phytab input</description>
3 <requirements>
4 <requirement type="package">raxml</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_raxml.py -i $sequence -e $evo -f $efile -T 4 > $stdout 2>&amp;1
8 </command>
9 <!-- if using a queuing system, make sure number of ppn in jobrunner matches threads as set above -->
10 <inputs>
11 <param format="tabular" name="sequence" type="data" label="PHYTAB sequence file"/>
12 <param name="evo" type="select" format="txt">
13 <label>Model of evolution to apply to all data partitions (-m)</label>
14 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
15 </param>
16 <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab-delimited file with partition name in first column, evolutionary model in the second column. Must be RAxML
17 valid model names. (optional)"/>
18 </inputs>
19 <outputs>
20 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
21 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
22 </outputs>
23 <tests>
24 </tests>
25 <help>
26 **What it does**
27 Accepts Phytab input file (one or multiple gene partitions). Runs RAxML using specified model or model file for each partition.
28
29 For phytab format description, see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
30
31 See RAxML for additional information: https://github.com/stamatak/standard-RAxML
32
33 -------
34 **Performance**
35 The extent to which runs are parallelized may be altered through the Galaxy jobrunner (command-line). The number of threads is set in this tool's XML command section.
36
37 -------
38 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
39
40 -------
41
42 **Citations**
43
44 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.
45
46 Current Osiris Citation is here
47
48 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
49
50 </help>
51 </tool>
52