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annotate lib/CPT/GalaxyGetOpt.pm @ 1:d724f34e671d draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:50:07 +0000
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1 package CPT::GalaxyGetOpt;
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2 use CPT::ParameterGroup;
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3 use autodie;
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4 use File::Spec::Functions qw[ catfile catdir ];
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5 use Carp;
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6 no warnings;
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7 use Moose;
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8
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9 has 'appdesc' => ( is => 'rw', isa => 'Str', default => sub { 'No application description provided' } );
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10 has 'appid' => ( is => 'rw', isa => 'Str', default => sub { "unknown_app_$0" } );
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11 has 'appname' => ( is => 'rw', isa => 'Str', default => sub { "Unnamed application $0"} );
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12 has 'appvers' => ( is => 'rw', isa => 'Str', default => sub { '0.0.1' } );
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13 has 'registered_outputs' => ( is => 'rw', isa => 'HashRef' );
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14 has 'opt' => ( is => 'rw', isa => 'Any');
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15 has filetype_detector => (
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16 is => 'rw',
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17 isa => 'Any',
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18 );
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19
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20
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21 sub getOptions {
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22 my ( $self, %passed_opts ) = @_;
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23 require Getopt::Long::Descriptive;
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24 # these get pushed through, thankfully. This way we can manually check for --genenrate_galaxy_export and exit slightly earlier.
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25 my %args = map { $_ => 1 } @ARGV;
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26 # Sections passed to us
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27 my @script_args = @{ $passed_opts{'options'} };
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28 my %defaults = @{ $passed_opts{'defaults'} };
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29
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30
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31
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32 # Output Files Stuff
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33 my @getopt_formatted_outputs;
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34 my %outputs;
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35 # This is originally an array of output files. We transform to a hash for
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36 # easier lookup
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37 foreach(@{$passed_opts{'outputs'}}){
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38 # Grab name/desc/opts
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39 my ($name, $desc, $opts) = @{$_};
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40 $outputs{$name} = {
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41 description => $desc,
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42 options => $opts,
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43 required => 1,
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44 };
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45 my %tmp_opts_fix = %{$opts};
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46 $tmp_opts_fix{required} = 1;
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47 $tmp_opts_fix{validate} = 'File/Output';
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48 push(@getopt_formatted_outputs, [$name, $desc, \%tmp_opts_fix]);
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49
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50 # Adds the {name}_files_path special parameter
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51 my %fp_opts = %{$opts};
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52 $fp_opts{hidden} = 1;
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53 $fp_opts{value} = "${name}.files_path";
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54 $fp_opts{default} = "${name}.files_path";
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55 $fp_opts{required} = 1;
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56 $fp_opts{_galaxy_specific} = 1;
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57 $fp_opts{validate} = "String";
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58 #$fp_opts{_show_in_galaxy} = 0;
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59 my $desc2 = "Associated HTML files for $name";
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60 my $name2 = "${name}_files_path";
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61 my @files_path = ($name2, $desc2, \%fp_opts);
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62 push(@getopt_formatted_outputs, \@files_path);
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63
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64 # Adds the {name}_format special parameter
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65 my %fp_opts3 = %{$opts};
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66 #$fp_opts3{hidden} = 1;
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67 $fp_opts3{default} = $fp_opts3{"default_format"};
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68 $fp_opts3{validate} = "File/OutputFormat";
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69 $fp_opts{required} = 1;
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70 #$fp_opts3{_galaxy_specific} = 1;
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71 #$fp_opts3{_show_in_galaxy} = 0;
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72 my $desc3 = "Associated Format for $name";
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73 my $name3 = "${name}_format";
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74 my @files_path3 = ($name3, $desc3, \%fp_opts3);
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75 push(@getopt_formatted_outputs, \@files_path3);
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76
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77 # Adds the {name}_files_path special parameter
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78 my %fp_opts4 = %{$opts};
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79 $fp_opts4{hidden} = 1;
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80 $fp_opts4{value} = "${name}.id";
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81 $fp_opts4{default} = "${name}.id";
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82 $fp_opts4{validate} = "String";
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83 $fp_opts4{_galaxy_specific} = 1;
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84 #$fp_opts4{_show_in_galaxy} = 0;
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85 my $desc4 = "Associated ID Number for $name";
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86 my $name4 = "${name}_id";
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87 my @files_path4 = ($name4, $desc4, \%fp_opts4);
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88 push(@getopt_formatted_outputs, \@files_path4);
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89
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90 }
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91 $self->registered_outputs(\%outputs);
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92
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93
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94 # Store the application's name and description
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95 if($defaults{appdesc}){
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96 $self->appdesc($defaults{appdesc});
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97 }
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98 if($defaults{appid}){
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99 $self->appid($defaults{appid});
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100 }
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101 if($defaults{appname}){
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102 $self->appname($defaults{appname});
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103 }
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104 if($defaults{appvers}){
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105 $self->appvers($defaults{appvers});
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106 }
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107
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108 my $usage_desc;
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109 if ( $self->appname() && $self->appdesc() ) {
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110 $usage_desc = sprintf( "%s: %s\n%s [options] <some-arg>", $self->appname(), $self->appdesc(), $0 );
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111 }
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112
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113 # Individual parameter parsers
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114 require CPT::Parameter;
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115 # Which are stored in a collection of them
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116 require CPT::ParameterCollection;
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117
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118
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119 my $parameterCollection = CPT::ParameterCollection->new();
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120
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121 $parameterCollection->push_params(
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122 [
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123 #['Standard Options'],
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124 #@extra_params,
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125 #[],
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126 ['outfile_supporting' , 'File or folder to output to, necessary when (class == Report || multiple calls to classyReturnResults || multiple standalone output files)' , { hidden => 1, validate => 'String', default => '__new_file_path__', _galaxy_specific => 1, _show_in_galaxy => 0 }],
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127 ['galaxy' , 'Run with galaxy-specific overrides' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
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128 ['generate_galaxy_xml' , 'Generate a compatible galaxy-xml file. May need editing' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
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129 [],
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130 ['Script Options'],
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131 ]
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132 );
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133
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134 # If there's a default specified, we should apply that.
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135 foreach (@script_args) {
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136 # If it's an array, push as is, because either it's old style/label/empty
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137 # However, this doesn't allow setting defaults for things that aren't parameters
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138 # and it won't set defaults for old style
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139 if ( ref $_ eq 'ARRAY' ) {
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140 $parameterCollection->push_param($_);
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141 }elsif( ref $_ eq 'HASH'){
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142 my $pG = CPT::ParameterGroup->new();
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143 $pG->set_data($_);
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144 $parameterCollection->push_group($pG);
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145 }
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146 }
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147
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148 # Our magic output files stuff
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149 $parameterCollection->push_params(
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150 [
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151 [],
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152 ['Output Files'],
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153 @getopt_formatted_outputs,
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154 ]
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155 );
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156
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157 # Other standard options like verbosity/version/etc
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158 $parameterCollection->push_params(
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159 [
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160 [],
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161 ['Other Standard Options'],
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162 ['verbose|v', 'Be more verbose', {validate => 'Flag', _show_in_galaxy => 0}],
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163 ['version', 'Print version information', {validate => 'Flag', _show_in_galaxy => 0}],
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164 ['help', 'Print usage message and exit', {validate => 'Flag', _show_in_galaxy => 0}],
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165 ],
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166 );
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167
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168 # If we want the galaxy_xml, do that before the reduction step is called.
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169 if ( $args{'--version'} ) {
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170 print $self->appvers() . "\n";
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171 exit 1;
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172 }
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173
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174 # If we want the galaxy_xml, do that before the reduction step is called.
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175 if ( $args{'--generate_galaxy_xml'} ) {
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176 require CPT::Galaxy;
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177 my $galaxy_xml_generator = CPT::Galaxy->new();
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178 $galaxy_xml_generator->gen(
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179 full_options => $parameterCollection,
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180 appdesc => $self->appdesc(),
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181 appid => $self->appid(),
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182 appname => $self->appname(),
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183 appvers => $self->appvers(),
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184 defaults => $passed_opts{'defaults'},
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185 outputs => $passed_opts{'outputs'},
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186 tests => $passed_opts{'tests'},
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187 );
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188 exit 1;
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189 }
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190
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191 if( $args{'--gen_test'} ){
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192 require CPT::GenerateTests;
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193 my $tgen = CPT::GenerateTests->new();
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194 if(defined $passed_opts{'tests'}){
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195 print $tgen->gen(@{$passed_opts{'tests'}});
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196 }else{
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197 print $tgen->gen_empty();
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198 }
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199 exit 0;
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200 }
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201
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202 # Now that the options_spec is complete, we reduce to something getopt will be happy with
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203 my @getopt_spec = $parameterCollection->getopt();
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204 #print STDERR Dumper \@getopt_spec;
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205 #exit 1;
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206
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207 # It would be nice if there was a way to ensure that it didn't die here...
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208 # Execute getopt
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209 my ( $local_opt, $usage ) = Getopt::Long::Descriptive::describe_options( $usage_desc, @getopt_spec );
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210 $self->opt($local_opt);
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211
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212 # Now that we've gotten the user's options, we need to copy their values back to our ParameterCollection
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213 $parameterCollection->populate_from_getopt($self->opt());
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214
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215 # If they want help, print + exit
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216 if ( $self->opt && $self->opt->help ) {
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217 print $usage;
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218 exit 1;
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219 }
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220 # Validate their choices
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221 if ( $parameterCollection->validate($self->opt) ) {
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222 return $self->opt;
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223 # Easy access for the script, don't want them to have to deal with PC (just yet)
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224 }
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225 else {
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226 # Some params failed to validate, so we die.
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227 croak "Validation errors were found so cannot continue";
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228 }
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229 }
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230
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231 no Moose;
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232 1;
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233
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234 __END__
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235
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236 =pod
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237
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238 =encoding UTF-8
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239
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240 =head1 NAME
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241
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242 CPT::GalaxyGetOpt
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243
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244 =head1 VERSION
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245
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246 version 1.99.4
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247
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248 =head2 getOptions
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249
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250 my $ggo = CPT::GalaxyGetOpt->new();
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251 my $options = $ggo->getOptions(
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252 'options' => [
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253 [ 'file', 'Input file', { validate => 'File/Input' } ],
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254 [
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255 "option" => "Select an option!",
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256 {
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257 validate => 'Option',
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258 options => \%options,
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259 multiple => 1,
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260 }
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261 ],
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262 [
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263 "float" => "I'm a float",
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264 { validate => 'Float' }
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265 ],
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266 [
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267 "int" => "I'm an int",
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268 { validate => 'Int', default => [42, 34], required => 1, multiple => 1 }
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269 ],
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270 [],
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271 ['New section'],
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272 [
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273 "string" => "I'm a simple string",
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274 { validate => 'String' }
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275 ],
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276 [
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277 'flag' => 'This is a flag',
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278 { validate => 'Flag' }
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279 ],
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280 ],
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281 'outputs' => [
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282 [
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283 'my_output_data',
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284 'Output TXT File',
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285 {
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286 validate => 'File/Output',
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287 required => 1,
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288 default => 'out',
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289 data_format => 'text/plain',
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290 default_format => 'TXT',
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291 }
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292 ],
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293 ],
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294 'defaults' => [
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295 'appid' => 'TemplateScript',
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296 'appname' => 'Template',
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297 'appdesc' => 'A basic template for a new CPT application',
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298 'appvers' => '1.94',
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299 ],
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300 'tests' => [
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301 {
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302 test_name => "Default",
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303 params => {
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304 },
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305 outputs => {
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306 'my_output_data' => ["out.txt", 'test-data/outputs/template.default.txt' ],
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307 },
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308 },
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309 {
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310 test_name => "Option A specified",
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311 params => {
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312 'int', '10000',
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313 },
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314 outputs => {
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315 'my_output_data' => ["out.txt", 'test-data/outputs/template.A.txt' ],
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316 },
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317 },
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318 ],
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319 );
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320
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321 my @data;
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322 foreach(qw(file int string option float flag)){
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323 # Create a 2D array of all of our optoins
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324 push(@data, [ $_, $options->{$_}]);
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325 }
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326
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327 my %table = (
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328 'Sheet1' => {
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329 header => [qw(Key Value)],
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330 data => \@data,
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331 }
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332 );
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333
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334 # And store it to file!
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335 use CPT::OutputFiles;
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336 my $crr_output = CPT::OutputFiles->new(
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337 name => 'my_output_data',
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338 GGO => $ggo,
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339 );
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340 $crr_output->CRR(data => \%table);
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341
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342 Gets command line options, and prints docs. Very convenient, removes the burden of writing any Getopt code from you.
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343
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344 =head3 Default Options Provided
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345
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346 =over 4
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347
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348 =item *
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349
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350 help, man - cause an early exit and printing of the POD for your script.
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351
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352 =item *
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353
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354 verbose - flag to make the script verbose. Will print everything that is sent to returnResults. Individual scripts should take advantage of this option
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355
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356 =back
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357
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358 =head3 Advanced Options Provided
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359
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360 =over 4
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361
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362 =item C<--generate_galaxy_xml>
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363
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364 Generates valid XML for the tool for use in Galaxy
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365
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366 =item C<--gen_test>
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367
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368 Generates code to test the script using specified test data
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369
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370 =back
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371
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372 =head1 AUTHOR
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373
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374 Eric Rasche <rasche.eric@yandex.ru>
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375
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376 =head1 COPYRIGHT AND LICENSE
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377
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378 This software is Copyright (c) 2014 by Eric Rasche.
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379
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380 This is free software, licensed under:
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381
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382 The GNU General Public License, Version 3, June 2007
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383
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384 =cut