Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison phylogenies/raxml_pars.pl @ 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 #! /usr/bin/perl -w
2
3 use strict;
4 use warnings;
5 #raxml.pl Galaxy wrapper calls raxml from raxml.xml
6
7 #For debugging command line pass, uncomment next 4 lines
8 #for (my $i=0; $i < @ARGV; $i++){
9 # print "Parameter #$i ".$ARGV[$i]."\n\n";
10 #}
11 #exit;
12
13 my $datatype = shift(@ARGV); #0 datatype
14 my $data_file= shift(@ARGV); #1 input a phylip file
15 my $part_file = shift(@ARGV); #2 optional partition file
16 my $seed = shift(@ARGV); #3 Number of bootstrap reps
17 my $outgroup = shift(@ARGV); #4 Specify the outgroup
18 my $model;
19
20 #ADD OPTIONS TO BUILD FULL RAXML COMMANDLINE ARGUMENT
21
22 my $build_command;
23 #First CALL RAXML THROUGH PATH with 8 threads
24 $build_command = "raxmlHPC-PTHREADS-SSE3 ";
25 #Add Parsimony Option and Thread number for PThreads
26 $build_command = $build_command." -y -T 4";
27 #Next add call to input phylip file
28 $build_command = $build_command." -s ".$data_file;
29 #Add call to partition file name
30 unless($part_file eq 'None'){
31 $build_command = $build_command." -q ".$part_file;
32 }
33 #model is passed directly with xml
34 $model = $datatype;
35 $build_command = $build_command." -m ".$model;
36 #Parsimony seed
37 $build_command = $build_command." -p ".$seed;
38 #name output files galaxy
39 $build_command = $build_command." -n parsimony";
40 #Outgroup
41 if(defined $outgroup){
42 $build_command = $build_command." -o ".$outgroup;
43 }
44
45 print "Galaxy COMMAND BUILD WAS: $build_command\n";
46
47 #Uncomment to actually call raxml
48 system $build_command;