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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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0:b8b8b52904a5 1:f093e08f21f3
1 package CPT::Parameter::File::Output;
2 use Moose;
3 with 'CPT::Parameter';
4 use CPT::OutputFiles;
5
6 # Has the user requested that the format is ALWAYS of a specific type. This is
7 # useful when (e.g,.) CSV output is required because it's part of a pipeline.
8 # Of course, in a perfect world that wouldn't be necessary as we'd be able to
9 # read in data and the only constraint would be that it was "text/tabular" and
10 # magically we'd have a hash just like we would with CSV. Sigh....
11 has 'hardcoded' => ( is => 'rw', isa => 'Bool' );
12 # The format of the internal data structure that we're pushing to output
13 # See CPT.pm for a list of these (under %acceptable)
14 has 'data_format' => ( is => 'rw', isa => 'Str' );
15 has 'default_format' => ( is => 'rw', isa => 'Str' );
16
17 # registered => ['text/tabular~CSV', 'text/plain=TXT'],
18 has 'registered_types' => ( is => 'rw', isa => 'ArrayRef' );
19 has 'cpt_outputfile_data_access' => ( is => 'ro', isa => 'Any', default => sub { CPT::OutputFiles->new() } );
20
21
22
23 sub galaxy_input {
24
25 # Required by our parent. For an output file, this is non-functional
26 my ( $self, $xml_writer ) = @_;
27 $self->handle_possible_galaxy_input_repeat_start($xml_writer);
28 my %params = $self->get_default_input_parameters('select');
29 $params{label} = 'Format of ' . $self->get_galaxy_cli_identifier(),
30 $params{name} = sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
31 # Remove any default values for galaxy
32 delete $params{value};
33 $xml_writer->startTag(
34 'param',
35 %params,
36 );
37
38 if(defined $self->data_format()){
39
40 foreach ( sort @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) } ) {
41 my %p = (value => $_);
42 if($_ eq $self->default_format()){
43 $p{selected} = 'True';
44 }
45 $xml_writer->startTag( 'option', %p );
46 $xml_writer->characters( $_ );
47 $xml_writer->endTag('option');
48 }
49 }else{
50 $xml_writer->startTag( 'option', value => 'data', selected => 'True' );
51 $xml_writer->characters( 'data' );
52 $xml_writer->endTag('option');
53 }
54 $xml_writer->endTag('param');
55 $self->handle_possible_galaxy_input_repeat_end($xml_writer);
56 }
57
58
59 sub galaxy_output {
60 my ( $self, $xml_writer ) = @_;
61 my $format;
62 if(defined $self->default_format()){
63 $format = $self->default_format();
64 }else{
65 $format = 'data';
66 }
67
68 $xml_writer->startTag(
69 'data',
70 name => $self->get_galaxy_cli_identifier(),
71 format => $format,
72 );
73
74 if ( !$self->hardcoded() ) {
75 $xml_writer->startTag('change_format');
76 # Otherwise it's still going to be set as the default_format so we're not toooo worried.
77 if(defined($self->data_format())){
78 my @galaxy_formats = @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) };
79 foreach (sort @galaxy_formats) {
80 $xml_writer->startTag(
81 'when',
82 input => sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
83 value => $_,
84 format => $self->cpt_outputfile_data_access()->get_format_mapping($_),
85 );
86 $xml_writer->endTag('when');
87 }
88 }
89 $xml_writer->endTag('change_format');
90 }
91 $xml_writer->endTag('data');
92 }
93
94 sub validate_individual {
95 my ($self, $val) = @_;
96 #if(! -e $self->value()){
97 # return 1;
98 #}
99 #return 0;
100 return 1;
101 }
102
103
104 sub getopt_format {
105 return '=s';
106 }
107
108 no Moose;
109 1;
110
111 __END__
112
113 =pod
114
115 =encoding UTF-8
116
117 =head1 NAME
118
119 CPT::Parameter::File::Output
120
121 =head1 VERSION
122
123 version 1.99.4
124
125 =head2 galaxy_input
126
127 $file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::*
128
129 Utilises the $xml_writer to add a <data> block in the <output> section
130
131 =head2 galaxy_output
132
133 $file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::*
134
135 Utilises the $xml_writer to add a <data> block in the <output> section
136
137 =head2 getopt_format
138
139 Returns the format character for a given CPT::Parameter::* type
140
141 =head1 AUTHOR
142
143 Eric Rasche <rasche.eric@yandex.ru>
144
145 =head1 COPYRIGHT AND LICENSE
146
147 This software is Copyright (c) 2014 by Eric Rasche.
148
149 This is free software, licensed under:
150
151 The GNU General Public License, Version 3, June 2007
152
153 =cut