tree_relabeler: nml_tree_relabeler.pl annotate

annotate nml_tree_relabeler.pl @ 2:41ada87567a2 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 8ad15943a8d365b3924ff7a5e53308cc56d7a6af

author	nml
date	Thu, 27 Jun 2019 15:03:13 -0400
parents	02bc0d7d40b5
children

rev	line source
0 02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	1 #!/usr/bin/env perl
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	2
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	3 use strict;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	4 use warnings;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	5 use Bio::TreeIO;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	6 use Bio::Tree::Tree;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	7 use IO::String;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	8 use Getopt::Long;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	9 use Pod::Usage;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	10
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	11 my ($treefile, $tabfile, $delim, $outfile, $template, $help, $replace, $tabline, $man );
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	12
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	13 GetOptions(
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	14 'i\|treefile=s' => \$treefile,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	15 't\|tabfile=s' => \$tabfile,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	16 'o\|outfile=s' => \$outfile,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	17 'd\|delim:s' => \$delim,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	18 'p\|print-template=s' => \$template,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	19 'r\|replace' => \$replace,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	20 'h\|help' => \$help,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	21 'm\|man' => \$man
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	22 );
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	23
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	24 if ($help){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	25 pod2usage(-verbose => 99,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	26 -sections => "SYNOPSIS\|OPTIONS AND ARGUMENTS\|DESCRIPTION\|DIAGNOSTICS");
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	27 } elsif ($man){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	28 pod2usage(-verbose => 2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	29 } elsif (!$treefile) {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	30 pod2usage(-msg => "Tree file is required.\n",
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	31 -exitval => 2,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	32 -verbose => 1,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	33 -output => \*STDERR);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	34 } elsif ( !(($template) \|\| ($tabfile && $outfile)) ){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	35 pod2usage(-msg => "Either select a template file, or a tab file and outfile\n",
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	36 -exitval => 2,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	37 -verbose => 1,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	38 -output => \*STDERR);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	39 } elsif ( $treefile && $template) {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	40 generate_template();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	41 } elsif ( $treefile && $tabfile && $outfile ){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	42 relabel_tree();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	43 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	44
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	45 sub generate_template
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	46 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	47 check_treefile();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	48 print_template();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	49 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	50
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	51 sub relabel_tree
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	52 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	53 my %new_labels;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	54 check_delimiter();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	55 %new_labels = %{load_tabfile()};
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	56 check_treefile();
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	57 write_treefile(\%new_labels);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	58 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	59
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	60 sub print_template
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	61 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	62 open my $tempout, '>', $template or die "Could not open file: $!";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	63 print $tempout "#label\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	64
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	65 my $treein = Bio::TreeIO->new(
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	66 -format => "newick",
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	67 -file => "$treefile"
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	68 );
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	69
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	70 while(my $t = $treein->next_tree)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	71 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	72 my @nodes = $t->get_nodes;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	73
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	74 if (scalar(@nodes) <= 1)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	75 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	76 print STDERR "Tree is not in newick format.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	77 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	78 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	79 else
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	80 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	81 foreach my $node ($t->get_leaf_nodes)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	82 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	83 print $tempout $node->id,"\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	84 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	85 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	86 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	87 close ($tempout);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	88 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	89
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	90 sub check_delimiter
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	91 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	92 if (!($delim)){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	93 $delim = ' ';
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	94 } else{
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	95 my $delimlen = length $delim;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	96 # delim length less than 1 indicates empty string.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	97 if ($delimlen < 1){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	98 $delim = ' ';
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	99 }elsif ($delim =~ /[\;\,\:]/){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	100 print STDERR "Delimiters cannot be Newick reserved characters '(),;:'.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	101 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	102 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	103 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	104 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	105
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	106 sub load_tabfile
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	107 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	108 my %new_labels;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	109 if (!(-e $tabfile)){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	110 # exit if error in tab file
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	111 print STDERR "Error opening tab file.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	112 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	113 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	114
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	115 open (my $tabin, '<', $tabfile);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	116
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	117 # append the > to the front of the outfile string
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	118 # $outfile = '>'.$outfile;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	119
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	120 # go through tab file to add new labels to a hash file
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	121 while ($tabline = <$tabin>){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	122 # skip the first row if it starts with a #
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	123 next if $tabline =~ s/^#//;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	124 $tabline =~ s/\r//g;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	125 chomp $tabline;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	126
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	127 if ($tabline =~ /[\;\,\:]/){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	128 print STDERR "New labels cannot contain Newick reserved characters '(),;:'.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	129 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	130 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	131
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	132 my @splits = split("\t", $tabline);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	133
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	134 # Check that the tab file has more than one column
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	135 my $num_cols = scalar @splits;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	136 if ($num_cols <= 1){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	137 # exit if one column or less; no new info to add to tree/error with tab layout.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	138 print STDERR "Tab file does not contain new labels.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	139 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	140 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	141 # set the hash label to the first value in a row, is the original tip label.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	142 my $label = $splits[0];
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	143 # If user chose find and replace instead, get rid of the first value.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	144 shift @splits if ($replace);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	145 # join all values from @split into one string with delim separating them
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	146 my $new_info = join($delim, @splits);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	147 # add the new info to the hash
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	148 $new_labels{$label} = $new_info;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	149 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	150
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	151 close ($tabin);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	152
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	153 return \%new_labels;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	154 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	155
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	156 sub check_treefile
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	157 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	158 if (!(-e $treefile)){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	159 # exit if error in tree file
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	160 print STDERR "Error opening tree file.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	161 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	162 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	163
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	164
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	165 # open tree file to check format
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	166 if (!(-e $treefile)){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	167 # exit if error in tab file
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	168 print STDERR "Error opening tree file.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	169 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	170 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	171 if (-z $treefile){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	172 print STDERR "Tree file is empty.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	173 exit(1);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	174 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	175 my $linecount = 0;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	176 open (my $treein, '<', $treefile);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	177 my $line = <$treein>;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	178 my $nextline = <$treein>;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	179 if (defined $nextline){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	180 print STDERR "Tree is not in newick format. More than one line\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	181 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	182 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	183 close ($treein);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	184
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	185 my @chars = split("",$line);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	186 my $lastelem = @chars-2;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	187 my $bracketcount = 0;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	188 # look for non-spaces at end of line
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	189 while($chars[$lastelem] eq " "){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	190 $lastelem--;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	191 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	192 if ($chars[$lastelem] ne ";"){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	193 # newick formats end in ;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	194 print STDERR "Tree is not in newick format. Does not end in ; \n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	195 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	196 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	197
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	198 foreach my $char (@chars){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	199 if ($char eq ")"){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	200 if ($bracketcount == 0){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	201 # There is a ) before a (
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	202 print STDERR "Tree is not in newick format. Missing a (\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	203 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	204 }else {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	205 $bracketcount--;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	206 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	207 }elsif ($char eq "("){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	208 $bracketcount++;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	209 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	210 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	211 if ($bracketcount != 0){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	212 # There were not equal number of ( and )
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	213 print STDERR "Tree is not in newick format. Brackets do not match. \n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	214 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	215 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	216 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	217
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	218 sub write_treefile
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	219 {
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	220 my $temp = shift;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	221 my %new_labels = %{$temp};
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	222
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	223 # open tree file as a tree
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	224 my $treeinput = Bio::TreeIO->new(
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	225 -file => "$treefile"
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	226 );
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	227
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	228 #create output tree file
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	229 my $treeoutput = Bio::TreeIO->new(
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	230 -format => "newick",
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	231 -file => ">$outfile"
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	232 );
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	233
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	234 while(my $t = $treeinput->next_tree ){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	235 # check if tree is valid
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	236 if (scalar($t->get_nodes)<=1){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	237 # if tree has only 1 or less nodes, then it's not in correct format
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	238 print STDERR "Tree is not in newick format.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	239 exit(2);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	240 } else{
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	241 foreach my $label(keys %new_labels){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	242 my $tip = $t->find_node(-id =>$label);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	243 if ($tip){
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	244 # if found, change to the new label
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	245 $tip->id($new_labels{$label});
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	246 print $label," found and changed.\n"
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	247 } else{
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	248 # if label from tab file is not found, notify the user
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	249 print $label," not found.\n";
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	250 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	251 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	252 $treeoutput->write_tree($t);
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	253 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	254 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	255 }
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	256
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	257 exit;
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	258
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	259 =head1 NAME
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	260
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	261 nml_tree_relabeler.pl - Changes the tip labels on a newick formatted tree
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	262
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	263 =head1 VERSION
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	264
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	265 This documentation refers to nml_tree_relabeler.pl version 0.0.2.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	266
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	267 =head1 SYNOPSIS
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	268
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	269 nml_tree_relabeler.pl -i treefile [-t tabfile -o outfile (-d delim) (-r) \| -p template]
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	270
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	271 =head1 OPTIONS AND ARGUMENTS
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	272
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	273 =over
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	274
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	275 =item B<-i>, B<--treefile>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	276
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	277 The name of the tree file containing the tree to adjust the tip laels. Only accepts trees in newick format. (required)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	278
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	279 =item B<-t>, B<--tabfile>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	280
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	281 The name of the tab delimited file containing current tip labels and the info to be replaced/added tothe labels. The first column must contain the current tree labels. Must not contain one of the Newick reserved characters '(),:;' (required option)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	282
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	283 =item B<-o>, B<--out>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	284
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	285 The output file. (required option)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	286
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	287 =item B<-d>, B<--delim>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	288
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	289 The character to use to divide the information of the labels. Must not be one of the Newick reserved characters '(),:;' (optional)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	290
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	291 =item B<-r>, B<--replace>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	292
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	293 Replace the tip names. This option will replace the tree tip names with the specified labels, instead of adding them to the tip name.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	294
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	295 =item B<-p>, B<--print-template>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	296
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	297 The name of the output template file. Prints out a template for the tabfile.(required option)
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	298
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	299 =item B<-h>, B<--help>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	300
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	301 To display help message
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	302
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	303 =item B<-m>, B<--man>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	304
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	305 To display manual
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	306
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	307 =back
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	308
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	309 =head1 DESCRIPTION
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	310
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	311 =over
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	312
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	313 nml_tree_relabeler takes a newick format tree file to modify tip labels and a tab-delimited file containing current tip labels and additional information to add to the tips in 2 or more columns. Header row of the tab delimited file must start with a '#'. An example is below:
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	314
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	315 #label outbreak year location
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	316 orgs1 outbreak1 year1 location1
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	317 orgs2 outbreak2 year2 location2
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	318
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	319 and so on.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	320
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	321 The information in the tab file is inserted into the tree file so the new information will appear on the tip labels.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	322
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	323 Alternatively, nml_tree_relabeler can print out the tip names to a tab-delimited template file.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	324
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	325 =back
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	326
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	327 =head1 DIAGNOSTICS
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	328
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	329 =over
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	330
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	331 =item B<Tree file, tab file, and output file are required>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	332
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	333 Use the proper command line arguments (-i, -t, -o respectively) to add the filenames of the tree file, tab file, and output file.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	334
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	335 =item B<Tree file is required>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	336
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	337 Use the -i command line argument to add the tree file.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	338
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	339 =itemB<Either select a template file, or a tab file and outfile>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	340
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	341 Use the proper command line arguments to either add a template file (-p) to print a tab template, or to add a tab file and an output file (-t, -o respectively) to relabel a tree.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	342
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	343 =item B<Label not found>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	344
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	345 A warning that a label provided in the tab file was not found in the tree file. Relabeling continues.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	346
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	347 =item B<Error opening tab/tree file>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	348
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	349 An error occured while opening the tab/tree file, please check path/file.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	350
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	351 =item B<Tree is not in newick format>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	352
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	353 The tree file does not appear to be in newick format. Please check file and convert if necessary.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	354
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	355 =item B<Tab file does not contain new labels>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	356
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	357 The tab file only contains one column and therefore does not have any additional information to add to the tree. Please check the tab file.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	358
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	359 =item B<Delimiter/tabfile cannot contain Newick reserved characters '(),;:' >
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	360
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	361 The tab file or delimiter selected contains one of the characters used in the Newick format. This will cause an error when trying to read the tree. Please modify your tab file or select a new delimiter.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	362
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	363 =back
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	364
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	365 =head1 CONFIGURATION AND ENVIRONMENT
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	366
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	367 =head1 DEPENDENCIES
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	368
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	369 =over
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	370
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	371 =item use Bio::TreeIO
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	372
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	373 =item use Bio::Tree::Tree
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	374
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	375 =back
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	376
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	377 =head1 INCOMPATIBILITIES
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	378
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	379 This script only works for NEWICK formatted trees. All other tree formats are not compatible.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	380
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	381 =head1 AUTHOR
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	382
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	383 Jen Cabral, <jencabral@gmail.com>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	384
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	385 =head1 BUGS AND LIMITATIONS
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	386
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	387 There are no known bugs in this module.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	388
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	389 Please report problems to Jen Cabral, <jencabral@gmail.com>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	390
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	391 =head1 COPYRIGHT & LICENSE
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	392
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	393 Copyright (C) 2015 by NML
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	394
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	395 This program is free software: you can redistribute it and/or modify
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	396 it under the terms of the GNU General Public License as published by
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	397 the Free Software Foundation, either version 3 of the License, or
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	398 (at your option) any later version.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	399
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	400 This program is distributed in the hope that it will be useful,
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	401 but WITHOUT ANY WARRANTY; without even the implied warranty of
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	402 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	403 GNU General Public License for more details.
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	404
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	405 You should have received a copy of the GNU General Public License
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	406 along with this program. If not, see <http://www.gnu.org/licenses/>
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	407
02bc0d7d40b5 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8 nml parents: diff changeset	408 =cut

Mercurial > repos > nml > tree_relabeler

annotate nml_tree_relabeler.pl @ 2:41ada87567a2 draft default tip