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