diff lib/CPT/Parameter/File/Output.pm @ 1:97ef96676b48 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/Parameter/File/Output.pm	Mon Jun 05 02:51:26 2023 +0000
@@ -0,0 +1,153 @@
+package CPT::Parameter::File::Output;
+use Moose;
+with 'CPT::Parameter';
+use CPT::OutputFiles;
+
+# Has the user requested that the format is ALWAYS of a specific type. This is
+# useful when (e.g,.) CSV output is required because it's part of a pipeline.
+# Of course, in a perfect world that wouldn't be necessary as we'd be able to
+# read in data and the only constraint would be that it was "text/tabular" and
+# magically we'd have a hash just like we would with CSV. Sigh....
+has 'hardcoded' => ( is => 'rw', isa => 'Bool' );
+# The format of the internal data structure that we're pushing to output
+# See CPT.pm for a list of these (under %acceptable)
+has 'data_format' => ( is => 'rw', isa => 'Str' );
+has 'default_format' => ( is => 'rw', isa => 'Str' );
+
+# registered => ['text/tabular~CSV', 'text/plain=TXT'],
+has 'registered_types' => ( is => 'rw', isa => 'ArrayRef' );
+has 'cpt_outputfile_data_access' => ( is => 'ro', isa => 'Any', default => sub { CPT::OutputFiles->new() } );
+
+
+
+sub galaxy_input {
+
+	# Required by our parent. For an output file, this is non-functional
+	my ( $self, $xml_writer ) = @_;
+	$self->handle_possible_galaxy_input_repeat_start($xml_writer);
+	my %params = $self->get_default_input_parameters('select');
+	$params{label} = 'Format of ' . $self->get_galaxy_cli_identifier(),
+	$params{name} = sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
+	# Remove any default values for galaxy
+	delete $params{value};
+	$xml_writer->startTag(
+		'param',
+		%params,
+	);
+
+	if(defined $self->data_format()){
+
+		foreach ( sort @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) } ) {
+			my %p = (value => $_);
+			if($_ eq $self->default_format()){
+				$p{selected} = 'True';
+			}
+			$xml_writer->startTag( 'option', %p );
+			$xml_writer->characters( $_ );
+			$xml_writer->endTag('option');
+		}
+	}else{
+		$xml_writer->startTag( 'option', value => 'data', selected => 'True' );
+		$xml_writer->characters( 'data' );
+		$xml_writer->endTag('option');
+	}
+	$xml_writer->endTag('param');
+	$self->handle_possible_galaxy_input_repeat_end($xml_writer);
+}
+
+
+sub galaxy_output {
+	my ( $self, $xml_writer ) = @_;
+	my $format;
+	if(defined $self->default_format()){
+		$format = $self->default_format();
+	}else{
+		$format = 'data';
+	}
+
+	$xml_writer->startTag(
+		'data',
+		name   => $self->get_galaxy_cli_identifier(),
+		format => $format,
+	);
+
+	if ( !$self->hardcoded() ) {
+		$xml_writer->startTag('change_format');
+		# Otherwise it's still going to be set as the default_format so we're not toooo worried.
+		if(defined($self->data_format())){
+			my @galaxy_formats = @{ $self->cpt_outputfile_data_access()->valid_formats($self->data_format()) };
+			foreach (sort @galaxy_formats) {
+				$xml_writer->startTag(
+					'when',
+					input  => sprintf( "%s_%s", $self->get_galaxy_cli_identifier, 'format' ),
+					value  => $_,
+					format => $self->cpt_outputfile_data_access()->get_format_mapping($_),
+				);
+				$xml_writer->endTag('when');
+			}
+		}
+		$xml_writer->endTag('change_format');
+	}
+	$xml_writer->endTag('data');
+}
+
+sub validate_individual {
+	my ($self, $val) = @_;
+	#if(! -e $self->value()){
+	#	return 1;
+	#}
+	#return 0;
+	return 1;
+}
+
+
+sub getopt_format {
+	return '=s';
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::Parameter::File::Output
+
+=head1 VERSION
+
+version 1.99.4
+
+=head2 galaxy_input
+
+	$file_param->galaxy_input($xml_writer); # where $file_param is a CPT::Parameter::*
+
+Utilises the $xml_writer to add a <data> block in the <output> section
+
+=head2 galaxy_output
+
+	$file_param->galaxy_output($xml_writer); # where $file_param is a CPT::Parameter::*
+
+Utilises the $xml_writer to add a <data> block in the <output> section
+
+=head2 getopt_format
+
+Returns the format character for a given CPT::Parameter::* type
+
+=head1 AUTHOR
+
+Eric Rasche <[e-mail]>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut