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annotate lib/CPT/Parameter/File/Output.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::Parameter::File::Output;
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2 use Moose;
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3 with 'CPT::Parameter';
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4 use CPT::OutputFiles;
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5
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6 # Has the user requested that the format is ALWAYS of a specific type. This is
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7 # useful when (e.g,.) CSV output is required because it's part of a pipeline.
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8 # Of course, in a perfect world that wouldn't be necessary as we'd be able to
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9 # read in data and the only constraint would be that it was "text/tabular" and
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10 # magically we'd have a hash just like we would with CSV. Sigh....
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11 has 'hardcoded' => ( is => 'rw', isa => 'Bool' );
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12 # The format of the internal data structure that we're pushing to output
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13 # See CPT.pm for a list of these (under %acceptable)
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14 has 'data_format' => ( is => 'rw', isa => 'Str' );
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15 has 'default_format' => ( is => 'rw', isa => 'Str' );
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16
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17 # registered => ['text/tabular~CSV', 'text/plain=TXT'],
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18 has 'registered_types' => ( is => 'rw', isa => 'ArrayRef' );
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19 has 'cpt_outputfile_data_access' => ( is => 'ro', isa => 'Any', default => sub { CPT::OutputFiles->new() } );
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20
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22
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23 sub galaxy_input {
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24
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25 # Required by our parent. For an output file, this is non-functional
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26 my ( $self, $xml_writer ) = @_;
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27 $self->handle_possible_galaxy_input_repeat_start($xml_writer);
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28 my %params = $self->get_default_input_parameters('select');
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29 $params{label} = 'Format of ' . $self->get_galaxy_cli_identifier(),
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30 $params{name} = sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
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31 # Remove any default values for galaxy
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32 delete $params{value};
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33 $xml_writer->startTag(
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34 'param',
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35 %params,
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36 );
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37
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38 if(defined $self->data_format()){
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39
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40 foreach ( sort @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) } ) {
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41 my %p = (value => $_);
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42 if($_ eq $self->default_format()){
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43 $p{selected} = 'True';
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44 }
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45 $xml_writer->startTag( 'option', %p );
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46 $xml_writer->characters( $_ );
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47 $xml_writer->endTag('option');
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48 }
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49 }else{
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50 $xml_writer->startTag( 'option', value => 'data', selected => 'True' );
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51 $xml_writer->characters( 'data' );
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52 $xml_writer->endTag('option');
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53 }
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54 $xml_writer->endTag('param');
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55 $self->handle_possible_galaxy_input_repeat_end($xml_writer);
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56 }
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57
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58
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59 sub galaxy_output {
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60 my ( $self, $xml_writer ) = @_;
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61 my $format;
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62 if(defined $self->default_format()){
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63 $format = $self->default_format();
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64 }else{
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65 $format = 'data';
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66 }
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67
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68 $xml_writer->startTag(
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69 'data',
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70 name => $self->get_galaxy_cli_identifier(),
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71 format => $format,
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72 );
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73
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74 if ( !$self->hardcoded() ) {
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75 $xml_writer->startTag('change_format');
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76 # Otherwise it's still going to be set as the default_format so we're not toooo worried.
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77 if(defined($self->data_format())){
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78 my @galaxy_formats = @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) };
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79 foreach (sort @galaxy_formats) {
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80 $xml_writer->startTag(
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81 'when',
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82 input => sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
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83 value => $_,
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84 format => $self->cpt_outputfile_data_access()->get_format_mapping($_),
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85 );
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86 $xml_writer->endTag('when');
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87 }
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88 }
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89 $xml_writer->endTag('change_format');
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90 }
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91 $xml_writer->endTag('data');
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92 }
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93
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94 sub validate_individual {
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95 my ($self, $val) = @_;
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96 #if(! -e $self->value()){
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97 # return 1;
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98 #}
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99 #return 0;
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100 return 1;
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101 }
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102
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103
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104 sub getopt_format {
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105 return '=s';
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106 }
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107
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108 no Moose;
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109 1;
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110
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111 __END__
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112
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113 =pod
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114
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115 =encoding UTF-8
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116
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117 =head1 NAME
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118
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119 CPT::Parameter::File::Output
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120
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121 =head1 VERSION
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122
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123 version 1.99.4
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124
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125 =head2 galaxy_input
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126
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127 $file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::*
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128
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129 Utilises the $xml_writer to add a <data> block in the <output> section
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130
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131 =head2 galaxy_output
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132
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133 $file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::*
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134
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135 Utilises the $xml_writer to add a <data> block in the <output> section
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136
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137 =head2 getopt_format
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138
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139 Returns the format character for a given CPT::Parameter::* type
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140
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141 =head1 AUTHOR
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142
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143 Eric Rasche <rasche.eric@yandex.ru>
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144
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145 =head1 COPYRIGHT AND LICENSE
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146
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147 This software is Copyright (c) 2014 by Eric Rasche.
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148
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149 This is free software, licensed under:
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150
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151 The GNU General Public License, Version 3, June 2007
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152
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153 =cut