--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/GalaxyGetOpt.pm	Mon Jun 05 02:48:47 2023 +0000
@@ -0,0 +1,384 @@
+package CPT::GalaxyGetOpt;
+use CPT::ParameterGroup;
+use autodie;
+use File::Spec::Functions qw[ catfile catdir ];
+use Carp;
+no warnings;
+use Moose;
+
+has 'appdesc' => ( is => 'rw', isa => 'Str', default => sub { 'No application description provided' } );
+has 'appid'   => ( is => 'rw', isa => 'Str', default => sub { "unknown_app_$0" } );
+has 'appname' => ( is => 'rw', isa => 'Str', default => sub { "Unnamed application $0"} );
+has 'appvers' => ( is => 'rw', isa => 'Str', default => sub { '0.0.1' } );
+has 'registered_outputs' => ( is => 'rw', isa => 'HashRef' );
+has 'opt' => ( is => 'rw', isa => 'Any');
+has filetype_detector => (
+    is	    => 'rw',
+    isa 	=> 'Any',
+);
+
+
+sub getOptions {
+    my ( $self, %passed_opts ) = @_;
+    require Getopt::Long::Descriptive;
+    # these get pushed through, thankfully. This way we can manually check for --genenrate_galaxy_export and exit slightly earlier.
+    my %args = map { $_ => 1 } @ARGV;
+    # Sections passed to us
+    my @script_args = @{ $passed_opts{'options'} };
+    my %defaults    = @{ $passed_opts{'defaults'} };
+
+
+
+    # Output Files Stuff
+    my @getopt_formatted_outputs;
+    my %outputs;
+    # This is originally an array of output files. We transform to a hash for
+    # easier lookup
+    foreach(@{$passed_opts{'outputs'}}){
+        # Grab name/desc/opts
+        my ($name, $desc, $opts) = @{$_};
+        $outputs{$name} = {
+            description => $desc,
+            options => $opts,
+            required => 1,
+        };
+	my %tmp_opts_fix = %{$opts};
+	$tmp_opts_fix{required} = 1;
+	$tmp_opts_fix{validate} = 'File/Output';
+        push(@getopt_formatted_outputs, [$name, $desc, \%tmp_opts_fix]);
+
+        # Adds the {name}_files_path special parameter
+        my %fp_opts = %{$opts};
+        $fp_opts{hidden} = 1;
+        $fp_opts{value} = "${name}.files_path";
+        $fp_opts{default} = "${name}.files_path";
+        $fp_opts{required} = 1;
+        $fp_opts{_galaxy_specific} = 1;
+        $fp_opts{validate} = "String";
+        #$fp_opts{_show_in_galaxy} = 0;
+        my $desc2 = "Associated HTML files for $name";
+        my $name2 = "${name}_files_path";
+        my @files_path = ($name2, $desc2, \%fp_opts);
+        push(@getopt_formatted_outputs, \@files_path);
+
+        # Adds the {name}_format special parameter
+        my %fp_opts3 = %{$opts};
+        #$fp_opts3{hidden} = 1;
+        $fp_opts3{default} = $fp_opts3{"default_format"};
+        $fp_opts3{validate} = "File/OutputFormat";
+        $fp_opts{required} = 1;
+        #$fp_opts3{_galaxy_specific} = 1;
+        #$fp_opts3{_show_in_galaxy} = 0;
+        my $desc3 = "Associated Format for $name";
+        my $name3 = "${name}_format";
+        my @files_path3 = ($name3, $desc3, \%fp_opts3);
+        push(@getopt_formatted_outputs, \@files_path3);
+
+        # Adds the {name}_files_path special parameter
+        my %fp_opts4 = %{$opts};
+        $fp_opts4{hidden} = 1;
+        $fp_opts4{value} = "${name}.id";
+        $fp_opts4{default} = "${name}.id";
+        $fp_opts4{validate} = "String";
+        $fp_opts4{_galaxy_specific} = 1;
+        #$fp_opts4{_show_in_galaxy} = 0;
+        my $desc4 = "Associated ID Number for $name";
+        my $name4 = "${name}_id";
+        my @files_path4 = ($name4, $desc4, \%fp_opts4);
+        push(@getopt_formatted_outputs, \@files_path4);
+
+    }
+    $self->registered_outputs(\%outputs);
+
+
+    # Store the application's name and description
+    if($defaults{appdesc}){
+        $self->appdesc($defaults{appdesc});
+    }
+    if($defaults{appid}){
+        $self->appid($defaults{appid});
+    }
+    if($defaults{appname}){
+        $self->appname($defaults{appname});
+    }
+    if($defaults{appvers}){
+        $self->appvers($defaults{appvers});
+    }
+
+    my $usage_desc;
+    if ( $self->appname() && $self->appdesc() ) {
+        $usage_desc = sprintf( "%s: %s\n%s [options] <some-arg>", $self->appname(), $self->appdesc(), $0 );
+    }
+
+    # Individual parameter parsers
+    require CPT::Parameter;
+    # Which are stored in a collection of them
+    require CPT::ParameterCollection;
+
+
+    my $parameterCollection = CPT::ParameterCollection->new();
+
+    $parameterCollection->push_params(
+        [
+            #['Standard Options'],
+            #@extra_params,
+            #[],
+            ['outfile_supporting'   ,  'File or folder to output to, necessary when (class == Report || multiple calls to classyReturnResults || multiple standalone output files)'  ,  { hidden => 1, validate => 'String', default => '__new_file_path__', _galaxy_specific => 1, _show_in_galaxy => 0 }],
+            ['galaxy'               ,  'Run with galaxy-specific overrides'                                                                                                          ,  {validate => 'Flag'                      ,  hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
+            ['generate_galaxy_xml'  ,  'Generate a compatible galaxy-xml file. May need editing'                                                                                     ,  {validate => 'Flag'                      ,  hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
+            [],
+            ['Script Options'],
+        ]
+    );
+
+    # If there's a default specified, we should apply that.
+    foreach (@script_args) {
+        # If it's an array, push as is, because either it's old style/label/empty
+        # However, this doesn't allow setting defaults for things that aren't parameters
+        # and it won't set defaults for old style
+        if ( ref $_ eq 'ARRAY' ) {
+            $parameterCollection->push_param($_);
+        }elsif( ref $_ eq 'HASH'){
+            my $pG = CPT::ParameterGroup->new();
+            $pG->set_data($_);
+            $parameterCollection->push_group($pG);
+        }
+    }
+
+    # Our magic output files stuff
+    $parameterCollection->push_params(
+        [
+            [],
+            ['Output Files'],
+            @getopt_formatted_outputs,
+        ]
+    );
+
+    # Other standard options like verbosity/version/etc
+    $parameterCollection->push_params(
+        [
+            [],
+            ['Other Standard Options'],
+            ['verbose|v', 'Be more verbose', {validate => 'Flag', _show_in_galaxy => 0}],
+            ['version', 'Print version information', {validate => 'Flag', _show_in_galaxy => 0}],
+            ['help', 'Print usage message and exit', {validate => 'Flag', _show_in_galaxy => 0}],
+        ],
+    );
+
+    # If we want the galaxy_xml, do that before the reduction step is called.
+    if ( $args{'--version'} ) {
+        print $self->appvers() . "\n";
+        exit 1;
+    }
+
+    # If we want the galaxy_xml, do that before the reduction step is called.
+    if ( $args{'--generate_galaxy_xml'} ) {
+        require CPT::Galaxy;
+        my $galaxy_xml_generator = CPT::Galaxy->new();
+        $galaxy_xml_generator->gen(
+            full_options => $parameterCollection,
+            appdesc      => $self->appdesc(),
+            appid        => $self->appid(),
+            appname      => $self->appname(),
+            appvers      => $self->appvers(),
+            defaults     => $passed_opts{'defaults'},
+            outputs      => $passed_opts{'outputs'},
+            tests        => $passed_opts{'tests'},
+        );
+        exit 1;
+    }
+
+    if( $args{'--gen_test'} ){
+        require CPT::GenerateTests;
+        my $tgen = CPT::GenerateTests->new();
+        if(defined $passed_opts{'tests'}){
+            print $tgen->gen(@{$passed_opts{'tests'}});
+        }else{
+            print $tgen->gen_empty();
+        }
+        exit 0;
+    }
+
+    # Now that the options_spec is complete, we reduce to something getopt will be happy with
+    my @getopt_spec = $parameterCollection->getopt();
+    #print STDERR Dumper \@getopt_spec;
+    #exit 1;
+
+    # It would be nice if there was a way to ensure that it didn't die here...
+    # Execute getopt
+    my ( $local_opt, $usage ) = Getopt::Long::Descriptive::describe_options( $usage_desc, @getopt_spec );
+    $self->opt($local_opt);
+
+    # Now that we've gotten the user's options, we need to copy their values back to our ParameterCollection
+    $parameterCollection->populate_from_getopt($self->opt());
+
+    # If they want help, print + exit
+    if ( $self->opt && $self->opt->help ) {
+        print $usage;
+        exit 1;
+    }
+    # Validate their choices
+    if ( $parameterCollection->validate($self->opt) ) {
+        return $self->opt;
+        # Easy access for the script, don't want them to have to deal with PC (just yet)
+    }
+    else {
+        # Some params failed to validate, so we die.
+        croak "Validation errors were found so cannot continue";
+    }
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::GalaxyGetOpt
+
+=head1 VERSION
+
+version 1.99.4
+
+=head2 getOptions
+
+	my $ggo = CPT::GalaxyGetOpt->new();
+	my $options = $ggo->getOptions(
+		'options' => [
+			[ 'file', 'Input file', { validate => 'File/Input' } ],
+			[
+				"option" => "Select an option!",
+				{
+					validate => 'Option',
+					options  => \%options,
+					multiple => 1,
+				}
+			],
+			[
+				"float" => "I'm a float",
+				{ validate => 'Float' }
+			],
+			[
+				"int" => "I'm an int",
+				{ validate => 'Int', default => [42, 34], required => 1, multiple => 1 }
+			],
+			[],
+			['New section'],
+			[
+				"string" => "I'm a simple string",
+				{ validate => 'String' }
+			],
+			[
+				'flag' => 'This is a flag',
+				{ validate => 'Flag' }
+			],
+		],
+		'outputs' => [
+			[
+				'my_output_data',
+				'Output TXT File',
+				{
+					validate       => 'File/Output',
+					required       => 1,
+					default        => 'out',
+					data_format    => 'text/plain',
+					default_format => 'TXT',
+				}
+			],
+		],
+		'defaults' => [
+			'appid'   => 'TemplateScript',
+			'appname' => 'Template',
+			'appdesc' => 'A basic template for a new CPT application',
+			'appvers' => '1.94',
+		],
+		'tests' => [
+			{
+				test_name    => "Default",
+				params => {
+				},
+				outputs => {
+					'my_output_data' => ["out.txt", 'test-data/outputs/template.default.txt' ],
+				},
+			},
+			{
+				test_name    => "Option A specified",
+				params => {
+					'int', '10000',
+				},
+				outputs => {
+					'my_output_data' => ["out.txt", 'test-data/outputs/template.A.txt' ],
+				},
+			},
+		],
+	);
+
+	my @data;
+	foreach(qw(file int string option float flag)){
+		# Create a 2D array of all of our optoins
+		push(@data, [ $_, $options->{$_}]);
+	}
+
+	my %table = (
+		'Sheet1' => {
+			header => [qw(Key Value)],
+			data => \@data,
+		}
+	);
+
+	# And store it to file!
+	use CPT::OutputFiles;
+	my $crr_output = CPT::OutputFiles->new(
+		name => 'my_output_data',
+		GGO => $ggo,
+	);
+	$crr_output->CRR(data => \%table);
+
+Gets command line options, and prints docs. Very convenient, removes the burden of writing any Getopt code from you.
+
+=head3 Default Options Provided
+
+=over 4
+
+=item *
+
+help, man - cause an early exit and printing of the POD for your script.
+
+=item *
+
+verbose - flag to make the script verbose. Will print everything that is sent to returnResults. Individual scripts should take advantage of this option
+
+=back
+
+=head3 Advanced Options Provided
+
+=over 4
+
+=item C<--generate_galaxy_xml>
+
+Generates valid XML for the tool for use in Galaxy
+
+=item C<--gen_test>
+
+Generates code to test the script using specified test data
+
+=back
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=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