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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1 package CPT::Parameter;
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2 use Moose::Role;
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3 use strict;
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4 use warnings;
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5 use autodie;
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6 use Carp;
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7
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8 #requires 'galaxy_command';
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9 requires 'galaxy_input';
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10 requires 'galaxy_output';
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11 requires 'validate_individual';
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12 requires 'getopt_format';
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13
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14 # Long name for this parameter (mandatory)
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15 has 'name' => ( is => 'rw', isa => 'Str' );
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16
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17 # Short name for this paramter (optional)
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18 has 'short' => ( is => 'rw', isa => 'Str' );
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19 has 'multiple' => ( is => 'rw', isa => 'Bool' );
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20 has 'description' => ( is => 'rw', isa => 'Str' );
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21
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22 # Attr
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23 # Default supplied parameters
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24 has 'default' => ( is => 'rw', isa => 'Any' );
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25 # User supplied values
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26 has 'value' => ( is => 'rw', isa => 'Any' );
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27 has 'required' => ( is => 'rw', isa => 'Bool' );
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28 has 'hidden' => ( is => 'rw', isa => 'Bool' );
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29
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30 # Set of error messages to be returned
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31 has 'errors' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] } );
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32
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33 # Unimplemented
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34 # Are there any implications of setting this
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35 has 'implies' => ( is => 'rw', isa => 'ArrayRef' );
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36
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37 # Internal
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38 has '_index' => ( is => 'rw', isa => 'Int', default => 0 );
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39
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40 # Galaxy Specific
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41 has '_galaxy_specific' => (is => 'rw', isa => 'Bool', default => 0);
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42 # implies option is somehow intertwined with whether or not this is being produced for use in galaxy.
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43 has '_show_in_galaxy' => (is => 'rw', isa => 'Bool', default => 1);
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44 # This is a custom override. If the object is hidden by default, it will causae it to be shown. If the object is visible by default, it can cause it to be hidden.
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45
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46
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47
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48 sub galaxy_command {
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49 my ($self) = @_;
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50 my $value = $self->get_galaxy_command_identifier();
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51
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52 # If it's hidden, specific to galaxy, and hidden from galaxy users,
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53 # then it is safe to assume we've specified a SANE default.
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54 if($self->hidden() && $self->_galaxy_specific()){
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55 $value = $self->default();
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56 }
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57 my $string;
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58
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59 # If it's a repeat, we handle that
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60 $string .= $self->handle_possible_galaxy_command_repeat_start();
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61 # If it's required we set it to a value IF we have one. Otherwise value
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62 # will be the galaxy_identifier.
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63 if($self->required()){
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64 $string .= sprintf( '--%s "${%s}"' . "\n",
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65 $self->get_galaxy_cli_identifier(), $value
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66 );
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67 }else{
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68 # If
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69 # This code is only relevant if we're multiple, otherwise the loop will
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70 # not pass here
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71 if ( !$self->multiple() ){
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72 $string .= sprintf('#if $%s and $%s is not "None":' . "\n",
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73 $self->get_galaxy_cli_identifier(),
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74 $self->get_galaxy_cli_identifier()
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75 );
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76 }
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77 # Flag
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78 $string .= sprintf( '--%s "${%s}"'."\n",
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79 $self->get_galaxy_cli_identifier(),
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80 $value
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81 );
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82 # End
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83 if ( !$self->multiple() ){
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84 $string .= "#end if\n";
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85 }
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86 }
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87 $string .= $self->handle_possible_galaxy_command_repeat_end();
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88 return $string;
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89 }
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90
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91
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92
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93 sub getOptionsArray {
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94 my ($self) = @_;
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95 my @getoptions;
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96 push( @getoptions, $self->getopt_identifier() );
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97
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98 my $mod_desc = $self->description();
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99 if(defined $self->default()){
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100 if(ref $self->default() eq 'ARRAY'){
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101 $mod_desc .= sprintf(" (Default: %s)", join(",",@{$self->default()}));
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102 }else{
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103 $mod_desc .= sprintf(" (Default: %s)", $self->default());
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104 }
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105 }
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106 if(substr(blessed($self),0,22) eq 'CPT::Parameter::Option'){
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107 my %kv = %{$self->options()};
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108 my @k = keys(%kv);
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109 $mod_desc .= sprintf(" (Options: %s)",
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110 join(
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111 ", ",
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112 map { $kv{$_} . " [$_]" } @k
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113 )
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114 );
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115 }else{
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116 }
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117
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parents:
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118 push( @getoptions, $mod_desc );
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cpt
parents:
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119
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cpt
parents:
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120 # Values to copy over: required, hidden, default, values
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cpt
parents:
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121 my %attr = ();
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cpt
parents:
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122 if ( $self->required() ) {
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cpt
parents:
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123 $attr{required} = $self->required();
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124 }
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cpt
parents:
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125 if ( $self->hidden() ) {
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parents:
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126 $attr{hidden} = $self->hidden();
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127 }
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128 if ( $self->default() ) {
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parents:
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129 $attr{default} = $self->default();
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130 }
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131 push( @getoptions, \%attr );
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132 return \@getoptions;
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133 }
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parents:
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134
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cpt
parents:
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135
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parents:
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136 sub getopt_identifier {
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parents:
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137 my ($self) = @_;
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cpt
parents:
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138 if ( defined( $self->short() ) && length($self->short()) > 0 ) {
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139 return sprintf( "%s|%s%s%s", $self->name(), $self->short(), $self->getopt_format(), ( $self->multiple() ? '@' : '' ), );
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140 }
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141 else {
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142 return sprintf( "%s%s%s", $self->name(), $self->getopt_format(), ( $self->multiple() ? '@' : '' ), )
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parents:
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143
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144 }
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145 }
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parents:
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146
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cpt
parents:
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147
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parents:
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148 sub get_galaxy_command_identifier {
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parents:
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149 my ($self) = @_;
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parents:
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150 if($self->multiple()){
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parents:
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151 return sprintf('%s.%s', $self->get_repeat_idx_name(), $self->get_galaxy_cli_identifier());
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parents:
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152 }else{
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parents:
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153 return $self->get_galaxy_cli_identifier();
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parents:
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154 }
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parents:
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155 }
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cpt
parents:
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156
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cpt
parents:
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157
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parents:
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158 sub get_galaxy_cli_identifier {
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parents:
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159 my ($self) = @_;
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parents:
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160 return $self->name();
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parents:
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161 }
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cpt
parents:
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162
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cpt
parents:
diff changeset
163
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cpt
parents:
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164 sub is_optional {
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parents:
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165 my ($self) = @_;
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cpt
parents:
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166 # Want coerced to int.
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parents:
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167 #return !$self->required();
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parents:
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168 if($self->required()){
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parents:
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169 return 0;
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parents:
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170 }else{
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parents:
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171 return 1;
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parents:
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172 }
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parents:
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173 }
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parents:
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174
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cpt
parents:
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175
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parents:
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176 sub is_optional_galaxy {
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parents:
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177 my ($self) = @_;
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parents:
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178 return $self->is_optional() ? "True" : "False";
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parents:
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179 }
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cpt
parents:
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180
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cpt
parents:
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181
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cpt
parents:
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182 sub update_index {
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parents:
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183 my ($self) = @_;
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parents:
diff changeset
184 if($self->multiple()){
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parents:
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185 my $size = scalar( @{ $self->value() } );
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cpt
parents:
diff changeset
186 # E.g:
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parents:
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187 # [1,2,3] , size = 3
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cpt
parents:
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188 # index = 3
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cpt
parents:
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189 # size = 3-1 = 2
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cpt
parents:
diff changeset
190 # index -> 0
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cpt
parents:
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191 if ( $self->_index() ge $size - 1 ) {
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parents:
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192 $self->_index(0);
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parents:
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193 }
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cpt
parents:
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194 else {
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parents:
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195 $self->_index( $self->_index() + 1 );
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parents:
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196 }
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parents:
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197 }
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parents:
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198 }
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cpt
parents:
diff changeset
199
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cpt
parents:
diff changeset
200
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cpt
parents:
diff changeset
201 sub reset_index {
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cpt
parents:
diff changeset
202 my ($self) = @_;
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cpt
parents:
diff changeset
203 $self->_index(0);
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parents:
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204 }
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cpt
parents:
diff changeset
205
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cpt
parents:
diff changeset
206
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cpt
parents:
diff changeset
207 sub get_value {
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cpt
parents:
diff changeset
208 my ($self) = @_;
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cpt
parents:
diff changeset
209 if ( defined $self->value() ) {
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cpt
parents:
diff changeset
210 if ( $self->multiple ) {
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cpt
parents:
diff changeset
211 my @data = @{ $self->value() };
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cpt
parents:
diff changeset
212 return $data[ $self->_index() ];
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parents:
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213 }
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cpt
parents:
diff changeset
214 else {
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parents:
diff changeset
215 return $self->value();
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parents:
diff changeset
216 }
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parents:
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217 }else{
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cpt
parents:
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218 return;
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cpt
parents:
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219 }
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cpt
parents:
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220 }
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cpt
parents:
diff changeset
221
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cpt
parents:
diff changeset
222
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cpt
parents:
diff changeset
223 sub get_default {
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cpt
parents:
diff changeset
224 my ($self) = @_;
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cpt
parents:
diff changeset
225 if ( defined $self->default() ) {
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cpt
parents:
diff changeset
226 if ( $self->multiple ) {
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parents:
diff changeset
227 my @data = @{ $self->default() };
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parents:
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228 return $data[ $self->_index() ];
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parents:
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229 }
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parents:
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230 else {
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parents:
diff changeset
231 return $self->default();
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parents:
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232 }
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parents:
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233 }else{
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cpt
parents:
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234 return;
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parents:
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235 }
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cpt
parents:
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236 }
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cpt
parents:
diff changeset
237
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cpt
parents:
diff changeset
238
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cpt
parents:
diff changeset
239
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cpt
parents:
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240 sub validate {
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cpt
parents:
diff changeset
241 my ($self) = @_;
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cpt
parents:
diff changeset
242 if ( $self->multiple() ) {
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243 my $errors = 0;
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cpt
parents:
diff changeset
244 if( ref($self->value()) ne 'ARRAY' ){
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245 carp "Author specified a non-array default value for " . $self->name() . ", which allows multiple values. Script author should modify the default value to be an ArrayRef.";
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246 }
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parents:
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247 for my $val ( @{ $self->value() } ) {
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248 if($self->validate_individual($val) == 0){
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249 $errors++;
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250 }
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parents:
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251 }
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parents:
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252 # Must cast to number otherwise it returns "" which is bad since I use
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parents:
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253 # 1/0 as T/F (true = good, false = bad)
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254 return 0+($errors == 0);
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255 }
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256 else {
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257 return 0+$self->validate_individual($self->value());
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258 }
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parents:
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259 }
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parents:
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260
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cpt
parents:
diff changeset
261
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parents:
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262 sub get_repeat_idx_name {
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parents:
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263 my ($self) = @_;
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264 return 'item';
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parents:
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265 }
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parents:
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266
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cpt
parents:
diff changeset
267
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parents:
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268 sub get_repeat_name {
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parents:
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269 my ($self) = @_;
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parents:
diff changeset
270 if($self->multiple()){
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parents:
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271 return sprintf('repeat_%s', $self->get_galaxy_cli_identifier());
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parents:
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272 }else{
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parents:
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273 confess "Tried to get repeat name for non-multiple item";
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parents:
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274 }
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parents:
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275 }
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parents:
diff changeset
276
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cpt
parents:
diff changeset
277
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parents:
diff changeset
278 sub handle_possible_galaxy_input_repeat_start {
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diff changeset
279 my ($self, $xml_writer ) = @_;
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parents:
diff changeset
280 if ( $self->multiple() ) {
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parents:
diff changeset
281 my $title = $self->get_galaxy_cli_identifier();
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parents:
diff changeset
282 $title =~ s/_/ /g;
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parents:
diff changeset
283 # Convert To Title Case (http://www.davekb.com/browse_programming_tips:perl_title_case:txt)
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parents:
diff changeset
284 $title =~ s/(\w+)/\u\L$1/g;
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parents:
diff changeset
285 $xml_writer->startTag(
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cpt
parents:
diff changeset
286 'repeat',
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parents:
diff changeset
287 'name' => $self->get_repeat_name(),
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parents:
diff changeset
288 'title' => $title,
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cpt
parents:
diff changeset
289 );
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parents:
diff changeset
290 }
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parents:
diff changeset
291 }
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parents:
diff changeset
292
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cpt
parents:
diff changeset
293
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parents:
diff changeset
294 sub handle_possible_galaxy_input_repeat_end {
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parents:
diff changeset
295 my ($self, $xml_writer ) = @_;
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cpt
parents:
diff changeset
296 if ( $self->multiple() ) {
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parents:
diff changeset
297 $xml_writer->endTag('repeat');
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parents:
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298 }
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parents:
diff changeset
299 }
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parents:
diff changeset
300
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cpt
parents:
diff changeset
301
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cpt
parents:
diff changeset
302
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parents:
diff changeset
303 sub handle_possible_galaxy_command_repeat_start {
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cpt
parents:
diff changeset
304 my ( $self ) = @_;
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cpt
parents:
diff changeset
305 if($self->multiple()){
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parents:
diff changeset
306 return sprintf("#for \$%s in \$%s:\n",
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cpt
parents:
diff changeset
307 $self->get_repeat_idx_name(),
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cpt
parents:
diff changeset
308 $self->get_repeat_name()
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parents:
diff changeset
309 );
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parents:
diff changeset
310 }else{
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parents:
diff changeset
311 return '';
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parents:
diff changeset
312 }
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parents:
diff changeset
313 }
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cpt
parents:
diff changeset
314
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cpt
parents:
diff changeset
315
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cpt
parents:
diff changeset
316 sub handle_possible_galaxy_command_repeat_end {
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cpt
parents:
diff changeset
317 my ( $self ) = @_;
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parents:
diff changeset
318 if($self->multiple()){
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parents:
diff changeset
319 return "#end for\n";
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parents:
diff changeset
320 }else{
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cpt
parents:
diff changeset
321 return '';
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cpt
parents:
diff changeset
322 }
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cpt
parents:
diff changeset
323 }
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cpt
parents:
diff changeset
324
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cpt
parents:
diff changeset
325 sub get_default_input_parameters {
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cpt
parents:
diff changeset
326 my ( $self, $type ) = @_;
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cpt
parents:
diff changeset
327 my %params = (
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cpt
parents:
diff changeset
328 name => $self->get_galaxy_cli_identifier(),
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cpt
parents:
diff changeset
329 optional => $self->is_optional_galaxy(),
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cpt
parents:
diff changeset
330 label => $self->get_galaxy_cli_identifier(),
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cpt
parents:
diff changeset
331 help => $self->description(),
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cpt
parents:
diff changeset
332 type => $type,
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cpt
parents:
diff changeset
333 );
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cpt
parents:
diff changeset
334
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cpt
parents:
diff changeset
335 # Multiple values would return ARRAY(0xAAAAAAA) locations, so we have to
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cpt
parents:
diff changeset
336 # handle those semi-intelligently until galaxy can handle default values
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cpt
parents:
diff changeset
337 # for repeats
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cpt
parents:
diff changeset
338 if($self->multiple() && defined $self->default()){
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cpt
parents:
diff changeset
339 if(ref($self->default()) ne 'ARRAY'){
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cpt
parents:
diff changeset
340 carp "Author specified a non-array default value for " . $self->name() . ", which allows multiple values. Script author should modify the default value to be an ArrayRef.";
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cpt
parents:
diff changeset
341 }
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parents:
diff changeset
342 $params{value} = ${$self->default}[0];
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cpt
parents:
diff changeset
343 }elsif(!$self->multiple() && defined $self->default()){
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cpt
parents:
diff changeset
344 $params{value} = $self->default();
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parents:
diff changeset
345 }
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cpt
parents:
diff changeset
346
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cpt
parents:
diff changeset
347 return %params;
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cpt
parents:
diff changeset
348 }
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cpt
parents:
diff changeset
349
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parents:
diff changeset
350 no Moose::Role;
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cpt
parents:
diff changeset
351
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cpt
parents:
diff changeset
352 1;
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cpt
parents:
diff changeset
353
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parents:
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354 __END__
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parents:
diff changeset
355
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parents:
diff changeset
356 =pod
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cpt
parents:
diff changeset
357
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cpt
parents:
diff changeset
358 =encoding UTF-8
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cpt
parents:
diff changeset
359
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cpt
parents:
diff changeset
360 =head1 NAME
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cpt
parents:
diff changeset
361
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cpt
parents:
diff changeset
362 CPT::Parameter
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cpt
parents:
diff changeset
363
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cpt
parents:
diff changeset
364 =head1 VERSION
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365
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366 version 1.99.4
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367
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368 =head2 galaxy_command
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369
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370 $file_param->galaxy_command(); # where $file_param is a CPT::Parameter::*
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371
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372 Returns the portion of the command used in the <command/> block in galaxy XML files
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373
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374 =head2 getOptionsArray
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375
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376 When called on a CPT::Parameter::* object, it will collapse the object into a GetOpt::Long compatible array
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377
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378 =head2 getopt_identifier
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379
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380 Used for backwards compatability with existing defaults => { 'file|f=s' => "Blah" } format
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381
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382 =head2 get_galaxy_identifier
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383
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384 Returns the identifier associated with a given variable. This identifier is what the Cheetah template knows the variable as (given the correct context).
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385
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386 For non-multiple variables it should be the name of the variable.
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387
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388 For multiple variables it will reference the repeat item name and then the variable name (e.g., C< $item.label >)
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389
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390 =head2 get_galaxy_cli_identifier
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391
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392 Returns the command line identifier (i.e., the command line flag) associated
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393 with a given parameter. For a `--format` flag, this would return "format".
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394 This should work out of the box, as CLI parameters have the same name as we
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395 specify them with (even if they're repeated)
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396
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397 =head2 is_optional
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398
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399 If required, it is NOT optional; If not reqiured, it IS optional
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400
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401 =head2 is_optional_galaxy
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402
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403 Returns is_optional() as "True" or "False" for convenience and reduced code duplication
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404
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405 =head2 update_index
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406
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407 Convenience method to increment the index. This wraps around.
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408
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409 =head2 reset_index
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410
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411 convenience method to zero the index (i.e., the next get_value request will start at the beginning again)
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412
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413 =head2 get_value
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414
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415 Returns the value in the current index.
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416
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417 =head2 get_default
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418
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419 Returns the default in the current index. Something to note, please bear in
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420 mind this you are trying to access an array based on an index which wraps
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421 according to value() not according to default(). This means you may not reach
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422 the end of default/reach over the end of default depending on how many values
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423 the user actually passes
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424
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425 =head2 validate
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426
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427 Validation logic was eventually moved out here, as the logic for validaton is
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428 identical everywhere, and requires slightly different behaviour based on
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429 wheterh or not it's a single/multiple valued item.
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430
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431 =head2 get_repeat_idx_name
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432
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433 Function to obtain the name of the item as it is called inside the repeat. This
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434 is necessary to know which variable we are referring to within a loop.
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435
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436 =head2 get_repeat_name
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437
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438 Function to obtain the name of the repeat. It is necessary that this is used
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439 identically in the command section as well as in the input section.
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440
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441 =head2 handle_possible_galaxy_input_repeat_start
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442
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443 If the feature is repeated, this should automatically handle the start of that
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444 repeat
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445
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446 =head2 handle_possible_galaxy_input_repeat_end
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447
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448 If the feature is repeated, this should automatically handle the end of that
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449 repeat
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450
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451 =head2 handle_possible_galaxy_command_repeat_start
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452
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453 If the feature is repeated, this should automatically handle the start of that
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454 repeat with a
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455
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456 #for $item in $repeat_name:
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457
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458 =head2 handle_possible_galaxy_command_repeat_end
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459
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460 If the feature is repeated, this should automatically handle the end of that
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461 repeat with
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462
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463 #end for
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464
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465 =head1 AUTHOR
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466
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467 Eric Rasche <rasche.eric@yandex.ru>
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468
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469 =head1 COPYRIGHT AND LICENSE
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470
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471 This software is Copyright (c) 2014 by Eric Rasche.
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472
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473 This is free software, licensed under:
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474
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475 The GNU General Public License, Version 3, June 2007
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476
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477 =cut