Mercurial > repos > cpt > cpt_psm_plotter
annotate lib/CPT/Parameter/Option.pm @ 1:8691c1c61a8e draft default tip
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt | 
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| date | Mon, 05 Jun 2023 02:48:47 +0000 | 
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| rev | line source | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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1 package CPT::Parameter::Option; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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2 use Moose::Role; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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3 use strict; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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4 use warnings; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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5 use autodie; | 
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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
 
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6 with 'CPT::Parameter'; | 
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7 | 
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8 has 'options' => ( is => 'rw', isa => 'HashRef' ); | 
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9 # stored as {short => "some long text"} | 
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10 | 
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11 | 
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12 sub galaxy_input { | 
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13 my ( $self, $xml_writer ) = @_; | 
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14 $self->handle_possible_galaxy_input_repeat_start($xml_writer); | 
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15 my %params = $self->get_default_input_parameters('select'); | 
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16 $xml_writer->startTag( | 
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17 'param', | 
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18 %params, | 
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19 ); | 
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20 my %options = %{ $self->options() }; | 
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21 foreach ( sort( keys(%options)) ) { | 
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22 my %p = (value => $_); | 
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23 if(defined $_ && defined $self->default() && $_ eq $self->default()){ | 
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24 $p{selected} = 'True'; | 
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25 } | 
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26 $xml_writer->startTag( 'option', %p); | 
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27 $xml_writer->characters( $options{$_} ); | 
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28 $xml_writer->endTag('option'); | 
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29 } | 
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30 $xml_writer->endTag('param'); | 
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31 $self->handle_possible_galaxy_input_repeat_end($xml_writer); | 
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32 } | 
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33 | 
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34 | 
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35 sub galaxy_output { | 
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36 | 
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37 } | 
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38 | 
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39 sub validate_individual { | 
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40 my ($self, $val) = @_; | 
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41 my %options = %{ $self->options() }; | 
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42 if($options{$val}){ | 
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43 return 1; | 
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44 }{ | 
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45 push(@{$self->errors()}, sprintf( "Unknown value [%s] supplied to a option %s", $val,$self->name())); | 
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46 return 0; | 
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47 } | 
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48 } | 
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49 | 
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50 | 
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51 sub getopt_format { | 
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52 return '=s'; | 
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53 } | 
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54 | 
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55 no Moose::Role; | 
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56 1; | 
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57 | 
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58 __END__ | 
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59 | 
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60 =pod | 
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61 | 
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62 =encoding UTF-8 | 
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63 | 
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64 =head1 NAME | 
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65 | 
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66 CPT::Parameter::Option | 
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67 | 
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68 =head1 VERSION | 
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69 | 
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70 version 1.99.4 | 
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71 | 
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72 =head2 galaxy_input | 
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73 | 
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74 $file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::* | 
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75 | 
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76 Utilises the $xml_writer to add a <data> block in the <output> section | 
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77 | 
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78 =head2 galaxy_output | 
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79 | 
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80 $file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::* | 
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81 | 
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82 Utilises the $xml_writer to add a <data> block in the <output> section | 
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83 | 
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84 =head2 getopt_format | 
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85 | 
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86 Returns the format character for a given CPT::Parameter::* type | 
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87 | 
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88 =head1 AUTHOR | 
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89 | 
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90 Eric Rasche <rasche.eric@yandex.ru> | 
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91 | 
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92 =head1 COPYRIGHT AND LICENSE | 
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93 | 
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94 This software is Copyright (c) 2014 by Eric Rasche. | 
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95 | 
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96 This is free software, licensed under: | 
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97 | 
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98 The GNU General Public License, Version 3, June 2007 | 
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99 | 
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100 =cut | 
