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annotate lib/CPT/Parameter/File/Input.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::Input;
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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 has 'format' => ( is => 'rw', isa => 'Str' );
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6 has 'file_format' => ( is => 'rw', isa => 'ArrayRef' );
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7
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8 # Format is something like "fastq", "bam", etc.
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9 # This means when you write the parameter string it'll be
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10 # ['file|f=s', 'Input Bam File', { required => 1, format=> 'file/input/bam'} ]
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11 # Which will specify that you require a BAM file.
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12
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13
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14 sub galaxy_input {
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15 my ( $self, $xml_writer ) = @_;
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16 $self->handle_possible_galaxy_input_repeat_start($xml_writer);
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17 my %params = $self->get_default_input_parameters('data');
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18 if( defined $self->file_format() ){
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19 $params{format} = join( ',', @{$self->file_format()} );
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20 }
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21 $xml_writer->startTag(
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22 'param',
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23 %params
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24 );
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25 $xml_writer->endTag('param');
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26 $self->handle_possible_galaxy_input_repeat_end($xml_writer);
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27 }
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29
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30 sub galaxy_output {
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31 my ($self, $xml_writer) = @_;
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32 return $xml_writer;
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33 }
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34
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35
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36 sub validate_individual {
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37 my ($self, $val) = @_;
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38
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39 # Maybe do format validation here? Maybe?
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40 if ( -e $val ) {
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41 return 1;
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42 }else{
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43 push(@{$self->errors()}, sprintf( "File [%s] supplied to option %s does not exist", $val,$self->name()));
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44 return 0;
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45 }
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46 }
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47
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48
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49 sub getopt_format {
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50 return '=s';
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51 }
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52
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53 no Moose;
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54 1;
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55
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56 __END__
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57
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58 =pod
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59
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60 =encoding UTF-8
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61
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62 =head1 NAME
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63
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64 CPT::Parameter::File::Input
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65
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66 =head1 VERSION
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67
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68 version 1.99.4
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69
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70 =head2 galaxy_input
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71
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72 $file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::*
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73
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74 Utilises the $xml_writer to add a <data> block in the <output> section
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75
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76 =head2 galaxy_output
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77
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78 $file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::*
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79
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80 Utilises the $xml_writer to add a <data> block in the <output> section
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81
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82 =head2 getopt_format
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83
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84 Returns the format character for a given CPT::Parameter::* type
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85
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86 =head1 AUTHOR
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87
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88 Eric Rasche <rasche.eric@yandex.ru>
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89
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90 =head1 COPYRIGHT AND LICENSE
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91
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92 This software is Copyright (c) 2014 by Eric Rasche.
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93
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94 This is free software, licensed under:
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95
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96 The GNU General Public License, Version 3, June 2007
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97
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98 =cut