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comparison phylostatistics/SHtest.pl @ 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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-1:000000000000 0:5b9a38ec4a39
1 #! /usr/bin/perl -w
2
3 use strict;
4 use warnings;
5
6 ##For debugging command line pass, uncomment next
7 #for (my $i=0; $i < @ARGV; $i++){
8 # print "Parameter #$i ".$ARGV[$i]."\n\n";
9 #}
10 #exit;
11
12 my $datatype = shift(@ARGV); #0 datatype
13 my $data_file= shift(@ARGV); #1 input a phylip file
14 my $part_file = shift(@ARGV); #2 optional partition file
15 my $best_tree = shift(@ARGV); #3 best tree for SH comparison
16 my $alt_trees = shift(@ARGV); #4 Alternative tree(s) for SH comparison
17 my $model;
18
19 #ADD OPTIONS TO BUILD FULL RAXML COMMANDLINE ARGUMENT
20
21 my $build_command;
22 #First CALL RAXML THROUGH PATH with 8 threads
23 $build_command = "raxmlHPC-PTHREADS-SSE3 ";
24 #Add SH Test Option and Thread number for PThreads
25 $build_command = $build_command."-f h -T 4";
26 #Next add call to input phylip file
27 $build_command = $build_command." -s ".$data_file;
28 #model is passed directly with xml
29 $model = $datatype;
30 $build_command = $build_command." -m ".$model;
31 #Add call to partition file name
32 unless($part_file eq 'None'){
33 $build_command = $build_command." -q ".$part_file;
34 }
35 #Next add call to input best tree file
36 $build_command = $build_command." -t ".$best_tree;
37 #Next add call to input best tree file
38 $build_command = $build_command." -z ".$alt_trees;
39 #name output files galaxy
40 $build_command = $build_command." -n SH";
41
42 print "Galaxy COMMAND BUILD WAS: $build_command\n";
43
44 #Uncomment to actually call raxml
45 system $build_command;
46