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annotate phylostatistics/SHtest.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #! /usr/bin/perl -w
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 use strict;
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4 use warnings;
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5
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6 ##For debugging command line pass, uncomment next
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 #for (my $i=0; $i < @ARGV; $i++){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 # print "Parameter #$i ".$ARGV[$i]."\n\n";
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9 #}
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10 #exit;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $datatype = shift(@ARGV); #0 datatype
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13 my $data_file= shift(@ARGV); #1 input a phylip file
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14 my $part_file = shift(@ARGV); #2 optional partition file
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15 my $best_tree = shift(@ARGV); #3 best tree for SH comparison
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16 my $alt_trees = shift(@ARGV); #4 Alternative tree(s) for SH comparison
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $model;
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19 #ADD OPTIONS TO BUILD FULL RAXML COMMANDLINE ARGUMENT
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20
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21 my $build_command;
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22 #First CALL RAXML THROUGH PATH with 8 threads
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 $build_command = "raxmlHPC-PTHREADS-SSE3 ";
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24 #Add SH Test Option and Thread number for PThreads
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 $build_command = $build_command."-f h -T 4";
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26 #Next add call to input phylip file
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27 $build_command = $build_command." -s ".$data_file;
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28 #model is passed directly with xml
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29 $model = $datatype;
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30 $build_command = $build_command." -m ".$model;
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31 #Add call to partition file name
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32 unless($part_file eq 'None'){
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33 $build_command = $build_command." -q ".$part_file;
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34 }
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35 #Next add call to input best tree file
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36 $build_command = $build_command." -t ".$best_tree;
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37 #Next add call to input best tree file
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38 $build_command = $build_command." -z ".$alt_trees;
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39 #name output files galaxy
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40 $build_command = $build_command." -n SH";
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41
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42 print "Galaxy COMMAND BUILD WAS: $build_command\n";
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43
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44 #Uncomment to actually call raxml
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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45 system $build_command;
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