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annotate lib/CPT/Parameter/Flag.pm @ 1:f093e08f21f3 draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 package CPT::Parameter::Flag;
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2 use Moose;
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3 with 'CPT::Parameter';
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4
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5
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6
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7 sub galaxy_command {
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8 my ($self) = @_;
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9 my $value = $self->get_galaxy_command_identifier();
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10
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11 # If it's hidden, specific to galaxy, and hidden from galaxy users,
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12 # then it is safe to assume we've specified a SANE default.
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13 if($self->hidden() && $self->_galaxy_specific()){
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14 $value = $self->default();
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15 }
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16 my $string;
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17
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18 # If it's a repeat, we handle that
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19 $string .= $self->handle_possible_galaxy_command_repeat_start();
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20 # If it's required we set it to a value IF we have one. Otherwise value
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21 # will be the galaxy_identifier.
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22 if($self->required()){
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23 $string .= sprintf( '--%s' . "\n",
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24 $self->get_galaxy_cli_identifier()
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25 );
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26 }else{
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27 # If
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28 # This code is only relevant if we're multiple, otherwise the loop will
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29 # not pass here
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30 if ( !$self->multiple() ){
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31 $string .= sprintf('#if $%s:' . "\n",
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32 $self->get_galaxy_cli_identifier()
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33 );
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34 }
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35 # Flag
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36 $string .= sprintf( '--%s'."\n",
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37 $self->get_galaxy_cli_identifier(),
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38 );
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39 # End
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40 if ( !$self->multiple() ){
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41 $string .= "#end if\n";
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42 }
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43 }
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44 $string .= $self->handle_possible_galaxy_command_repeat_end();
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45 return $string;
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46 }
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47
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48
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49
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50 sub galaxy_input {
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51 my ( $self, $xml_writer ) = @_;
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52 $self->handle_possible_galaxy_input_repeat_start($xml_writer);
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53 my %params = $self->get_default_input_parameters('boolean');
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54 $params{falsevalue} = 'False';
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55 $params{truevalue} = 'True';
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56 if($self->default()){
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57 $params{checked} = 'True';
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58 }else{
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59 $params{checked} = '';
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60 }
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61 # Remove value since we use "checked" here
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62 delete $params{value};
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63
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64 $xml_writer->startTag(
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65 'param',
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66 %params,
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67 );
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68 $xml_writer->endTag('param');
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69 $self->handle_possible_galaxy_input_repeat_end($xml_writer);
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70 }
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71
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72
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73 sub galaxy_output {
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74
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75 }
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76
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77
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78 sub validate_individual {
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79 my ($self) = @_;
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80 return 1;
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81 }
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82
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83
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84 sub getopt_format {
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85 return '';
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86 }
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87
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88 no Moose;
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89 1;
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90
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91 __END__
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92
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93 =pod
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94
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95 =encoding UTF-8
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96
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97 =head1 NAME
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98
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99 CPT::Parameter::Flag
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100
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101 =head1 VERSION
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102
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103 version 1.99.4
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104
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105 =head2 galaxy_command
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106
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107 $file_param->galaxy_command(); # where $file_param is a CPT::Parameter::*
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108
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109 Returns the portion of the command used in the <command/> block in galaxy XML files
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110
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111 =head2 galaxy_input
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112
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113 $file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::*
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114
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115 Utilises the $xml_writer to add a <data> block in the <output> section
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116
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117 =head2 galaxy_output
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118
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119 $file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::*
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120
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121 Utilises the $xml_writer to add a <data> block in the <output> section
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122
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123 =head2 getopt_format
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124
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125 Returns the format character for a given CPT::Parameter::* type
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126
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127 =head1 AUTHOR
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128
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129 Eric Rasche <rasche.eric@yandex.ru>
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130
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131 =head1 COPYRIGHT AND LICENSE
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132
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133 This software is Copyright (c) 2014 by Eric Rasche.
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134
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135 This is free software, licensed under:
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136
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137 The GNU General Public License, Version 3, June 2007
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138
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139 =cut