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comparison phylogenies/phytab_raxml_using_ptree.serial.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_useMPtrees" name="Phytab RAxML using Starting trees" version="1">
2 <description>Phytab RAxML - optimize branch lengths on trees</description>
3 <requirements>
4 <requirement type="package">raxml</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_raxml_using_ptree.serial.py -i $phytabinput -e $evo -f $efile -t $startingPtreelist> $stdout 2>&amp;1
8 </command>
9 <inputs>
10 <param format="tabular" name="phytabinput" type="data" label="PHYTAB sequence file"/>
11 <param format="tabular" name="startingPtreelist" type="data" label="Starting trees" help="(e.g., tree list output from PHYTAB RAxML Parsimony.)"/>
12 <param name="evo" type="select" format="text">
13 <label>Model of evolution to apply to all data partitions (-m)</label>
14 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option
15 value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option
16 value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option
17 value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option
18 value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option
19 value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option
20 value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
21 </param>
22 <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab seperated file with partition name in first column, evolutionary model in the second column. Must be RAxML
23 valid model names. (optional)"/>
24
25 </inputs>
26 <outputs>
27 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
28 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
29 </outputs>
30 <tests>
31 </tests>
32 <help>
33
34 **What it does**
35
36 This tool estimates likelihood trees and branch lengths for a PHYTAB file using starting trees (e.g., parsimony trees) to accelerate tree estimation.
37
38 **Input requirements**
39
40 1. PHYTAB sequence file
41 2. Starting tree list: two tab-delimited columns with the partition(gene) name and its newick starting tree (generated by PHYTAB RAxML-Parsimony)::
42
43 geneA (((Species_a,Species_b),Species_c),Species_d);
44 geneB ((Species_a,Species_b),(Species_c,Species_d));
45
46 </help>
47 </tool>
48