diff phylogenies/raxml_pars.pl @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/raxml_pars.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,48 @@
+#! /usr/bin/perl -w
+
+use strict;
+use warnings;
+#raxml.pl Galaxy wrapper calls raxml from raxml.xml
+
+#For debugging command line pass, uncomment next 4 lines
+#for (my $i=0; $i < @ARGV; $i++){
+#	print "Parameter #$i ".$ARGV[$i]."\n\n";
+#}
+#exit;
+
+my $datatype = shift(@ARGV);		#0 datatype
+my $data_file= shift(@ARGV);		#1 input a phylip file
+my $part_file = shift(@ARGV);		#2 optional partition file
+my $seed = shift(@ARGV);		#3 Number of bootstrap reps
+my $outgroup = shift(@ARGV);		#4 Specify the outgroup
+my $model;
+
+#ADD OPTIONS TO BUILD FULL RAXML COMMANDLINE ARGUMENT
+
+my $build_command;
+#First CALL RAXML THROUGH PATH with 8 threads
+	$build_command = "raxmlHPC-PTHREADS-SSE3 ";
+#Add Parsimony Option and Thread number for PThreads
+	$build_command = $build_command." -y -T 4";
+#Next add call to input phylip file
+	$build_command = $build_command." -s ".$data_file;
+#Add call to partition file name
+	unless($part_file eq 'None'){
+		$build_command = $build_command." -q ".$part_file;
+	}
+#model is passed directly with xml
+	$model = $datatype;
+	$build_command = $build_command." -m ".$model;
+#Parsimony seed
+	$build_command = $build_command." -p ".$seed;
+#name output files galaxy
+	$build_command = $build_command." -n parsimony";
+#Outgroup
+	if(defined $outgroup){
+		$build_command = $build_command." -o ".$outgroup;
+	}
+
+print "Galaxy COMMAND BUILD WAS: $build_command\n";
+
+#Uncomment to actually call raxml
+system $build_command;