Mercurial > repos > cpt > cpt_psm_plotter
annotate lib/CPT/Circos/Conf.pm @ 1:8691c1c61a8e draft default tip
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt | 
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| date | Mon, 05 Jun 2023 02:48:47 +0000 | 
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| rev | line source | 
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8691c1c61a8e
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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1 package CPT::Circos::Conf; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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2 use strict; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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3 use warnings; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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4 use autodie; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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5 use Moose; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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6 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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7 # This parameter specifies that we should behave according to galaxy_override spec. | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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8 has data => ( | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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9 is => 'rw', | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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10 isa => 'ArrayRef', | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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11 default => sub { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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12 [] | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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13 }, | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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14 ); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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15 my @current_block = (); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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16 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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17 sub set { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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18 my ($self, $key, $value) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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19 $self->push_d(sprintf('%s = %s', $key, $value)); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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20 } | 
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21 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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22 sub start_block { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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23 my ($self, $block) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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24 $self->push_d(sprintf('<%s>', $block)); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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25 push(@current_block, $block); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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26 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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27 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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28 sub end_block { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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29 my ($self) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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30 $self->push_d(sprintf('</%s>', pop @current_block)); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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31 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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32 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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33 sub include { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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34 my ($self, $file) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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35 $self->push_d(sprintf('<<include %s>>', $file)); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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36 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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37 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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38 sub push_d { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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39 my ($self, $string) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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40 push(@{$self->data()}, $self->spaces_for_indent() . $string); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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41 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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42 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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43 sub spaces_for_indent { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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44 my ($self) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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45 if(scalar(@current_block) > 0){ | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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46 return ' ' x scalar(@current_block); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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47 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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48 return ''; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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49 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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50 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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51 sub finalize { | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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52 my ($self) = @_; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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53 if(scalar @current_block > 0){ | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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54 die 'Blocks [' . join(',', @current_block) . '] were not closed'; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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55 } | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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56 else{ | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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57 return join("\n", @{$self->data()}); | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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58 } | 
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59 } | 
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60 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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61 no Moose::Role; | 
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62 1; | 
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63 | 
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64 __END__ | 
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65 | 
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66 =pod | 
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67 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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68 =encoding UTF-8 | 
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69 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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70 =head1 NAME | 
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71 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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72 CPT::Circos::Conf | 
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73 | 
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74 =head1 VERSION | 
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75 | 
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76 version 1.99.4 | 
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77 | 
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78 =head1 AUTHOR | 
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79 | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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80 Eric Rasche <rasche.eric@yandex.ru> | 
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81 | 
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82 =head1 COPYRIGHT AND LICENSE | 
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83 | 
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84 This software is Copyright (c) 2014 by Eric Rasche. | 
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85 | 
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86 This is free software, licensed under: | 
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87 | 
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88 The GNU General Public License, Version 3, June 2007 | 
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89 | 
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90 =cut | 
