Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
annotate phylogenies/phytab_raxml_using_ptree.serial.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
---|---|
date | Tue, 11 Mar 2014 12:19:13 -0700 |
parents | |
children |
rev | line source |
---|---|
0
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
1 <tool id="phytab_raxml_useMPtrees" name="Phytab RAxML using Starting trees" version="1"> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
2 <description>Phytab RAxML - optimize branch lengths on trees</description> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
3 <requirements> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
4 <requirement type="package">raxml</requirement> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
5 </requirements> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
6 <command interpreter="python"> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
7 phytab_raxml_using_ptree.serial.py -i $phytabinput -e $evo -f $efile -t $startingPtreelist> $stdout 2>&1 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
8 </command> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
9 <inputs> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
10 <param format="tabular" name="phytabinput" type="data" label="PHYTAB sequence file"/> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
11 <param format="tabular" name="startingPtreelist" type="data" label="Starting trees" help="(e.g., tree list output from PHYTAB RAxML Parsimony.)"/> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
12 <param name="evo" type="select" format="text"> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
13 <label>Model of evolution to apply to all data partitions (-m)</label> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
14 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
15 value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
16 value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
17 value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
18 value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
19 value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
20 value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
21 </param> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
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 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
23 valid model names. (optional)"/> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
24 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
25 </inputs> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
26 <outputs> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
27 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" /> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
28 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" /> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
29 </outputs> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
30 <tests> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
31 </tests> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
32 <help> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
33 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
34 **What it does** |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
35 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
36 This tool estimates likelihood trees and branch lengths for a PHYTAB file using starting trees (e.g., parsimony trees) to accelerate tree estimation. |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
37 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
38 **Input requirements** |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
39 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
40 1. PHYTAB sequence file |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
41 2. Starting tree list: two tab-delimited columns with the partition(gene) name and its newick starting tree (generated by PHYTAB RAxML-Parsimony):: |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
42 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
43 geneA (((Species_a,Species_b),Species_c),Species_d); |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
44 geneB ((Species_a,Species_b),(Species_c,Species_d)); |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
45 |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
46 </help> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
47 </tool> |
5b9a38ec4a39
First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff
changeset
|
48 |