--- a/cpt_psm_prep/lib/CPT/Galaxy.pm	Tue Jul 05 05:38:34 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,284 +0,0 @@
-package CPT::Galaxy;
-use Moose;
-use strict;
-use warnings;
-use Data::Dumper;
-use autodie;
-
-
-sub gen {
-	my ( $self, %p ) = @_;
-	my $parameterCollection = $p{full_options};
-	my @opt_spec            = @{ $parameterCollection->params() };    # This feels bad?
-	my %defaults            = @{ $p{defaults} };
-	my @outputs             = @{ $p{outputs} };
-	my @tests;
-	if(defined $p{tests} && ref $p{tests} eq 'ARRAY'){
-	    @tests = @{ $p{tests} };
-	}
-
-	my $optional_output_file = $p{_output_file};
-
-	#my @registered_outputs = @{ $outputs{'registered'} };
-	my $appid   = $p{appid};
-	my $appname = $p{appname};
-	my $appdesc = $p{appdesc};
-	my $appvers = $p{appvers};
-
-	# Set up the XML Writer
-	require XML::Writer;
-	my $xml_writer;
-	if($optional_output_file){
-		$xml_writer = XML::Writer->new(OUTPUT => $optional_output_file);
-	}else{
-		$xml_writer = XML::Writer->new();
-	}
-
-	# Set up the tool element
-	$xml_writer->startTag(
-		'tool',
-		id      => $appid,
-		name    => $appname,
-		version => $appvers,
-	);
-
-	# Add all of our sections, passing a single xml_writer around.
-	$self->description_section($xml_writer,$appdesc);
-	$self->version_section($xml_writer);
-	$self->stdio_section($xml_writer);
-
-	$self->command_section($xml_writer,\@opt_spec);
-	$self->input_section($xml_writer,\@opt_spec);
-	$self->output_section($xml_writer,\@opt_spec);
-
-	$self->help_section($xml_writer);
-
-	$self->test_section($xml_writer, @tests);
-
-	$xml_writer->endTag('tool');
-	$xml_writer->end();
-	# End of tool xml conf
-	
-	# if OOF was set to 'self', that means it's stored internally, so we should return
-	if(defined $optional_output_file && $optional_output_file eq 'self'){
-		return $xml_writer->to_string;
-	}
-}
-
-sub test_section {
-	my ($self, $xml_writer, @test_cases) = @_;
-	$xml_writer->startTag('tests');
-	foreach my $test(@test_cases){
-		my %test_details = %{$test};
-		$xml_writer->startTag('test');
-		# Each test case has: name, params, outputs
-
-		# Params will be as they're specified on the command line, so they /should/ be okay to use in galaxy code.
-		my %params = %{$test_details{'params'}};
-		foreach(sort(keys(%params))){
-			# As written, will not handle multiply valued attributes
-			$xml_writer->startTag('param',
-				name  => $_,
-				value => $params{$_},
-			);
-			$xml_writer->endTag();
-		}
-		# outputs
-		my %outputs = %{$test_details{'outputs'}};
-		foreach(sort(keys(%outputs))){
-			# As written, will not handle multiple outputs well
-			# This bit of code because for every output there's a
-			# name you expect on the command line, and a file you
-			# want to compare against (galaxy mucks about with
-			# names so we don't have to worry about it. However,
-			# from the command line, we have to know the name of
-			# the output file we're going to produce so we can
-			# compare it against another copy of this file. It's
-			# less than ideal, but there's not much we can do.
-			my @output_cmp = @{$outputs{$_}};
-			$xml_writer->startTag('output',
-				name => $_,
-				file => $output_cmp[1],
-			);
-			$xml_writer->endTag();
-		}
-		$xml_writer->endTag();
-	}
-	$xml_writer->endTag();
-}
-
-sub description_section{
-	my ($self, $xml_writer, $appdesc) = @_;
-	$xml_writer->startTag('description');
-	$xml_writer->characters(sprintf('%s',$appdesc));
-	$xml_writer->endTag('description');
-}
-
-sub version_section{
-	my ($self, $xml_writer) = @_;
-	$xml_writer->startTag('version_command');
-	$xml_writer->characters("perl $0 --version");
-	$xml_writer->endTag('version_command');
-}
-sub stdio_section{
-	my ($self, $xml_writer) = @_;
-	$xml_writer->startTag('stdio');
-	$xml_writer->startTag(
-		'exit_code',
-		range => "1:",
-		level => "fatal",
-	);
-	$xml_writer->endTag('exit_code');
-	$xml_writer->endTag('stdio');
-}
-sub command_section{
-	###################
-	# COMMAND SECTION #
-	###################
-	my ($self, $xml_writer,$opt_spec_ref) = @_;
-	my @opt_spec = @{$opt_spec_ref};
-	$xml_writer->startTag(
-		'command',
-		interpreter      => 'perl',
-	);
-	my $command_string = join("\n", $0, '--galaxy','--outfile_supporting $__new_file_path__','');
-	foreach (@opt_spec) {
-		if(
-		    # not galaxy specific and we are not instructed to hide
-		    !$_->_galaxy_specific() && $_->_show_in_galaxy()
-		    ||
-		    # is galaxy specific and is hidden
-		    $_->_galaxy_specific() && $_->hidden() && $_->_show_in_galaxy() 
-		){
-		#if(!$_->hidden() || ){
-			my $command_addition = $_->galaxy_command();
-			if($command_addition){
-				$command_string .= $command_addition . "\n";
-			}
-		}
-	}
-	$xml_writer->characters($command_string);
-	$xml_writer->endTag('command');
-}
-sub input_section{
-	my ($self, $xml_writer,$opt_spec_ref) = @_;
-	my @opt_spec = @{$opt_spec_ref};
-	#################
-	# INPUT SECTION #
-	#################
-	$xml_writer->startTag('inputs');
-	foreach (@opt_spec) {
-		if(
-		    # not galaxy specific and we are not instructed to hide
-			!$_->hidden() && !$_->_galaxy_specific() && $_->_show_in_galaxy()
-		){
-			$_->galaxy_input($xml_writer);
-		}
-	}
-	$xml_writer->endTag('inputs');
-}
-sub output_section{
-	my ($self, $xml_writer,$opt_spec_ref) = @_;
-	my @opt_spec = @{$opt_spec_ref};
-	##################
-	# OUTPUT SECTION #
-	##################
-	$xml_writer->startTag('outputs');
-	foreach (@opt_spec) {
-		if(
-		    # not galaxy specific and we are not instructed to hide
-		    !$_->_galaxy_specific() && $_->_show_in_galaxy()
-		){
-			$_->galaxy_output($xml_writer);
-		}
-	}
-	$xml_writer->endTag('outputs');
-}
-sub help_section{
-	my ($self, $xml_writer) = @_;
-	################
-	# HELP SECTION #
-	################
-
-	$xml_writer->startTag('help');
-	# Here we incur some dependencies. D:
-	use IPC::Run3;
-	my ($in,$out,$err);
-	use File::Temp;
-	my $tempfile = File::Temp->new(
-		TEMPLATE => 'libcpt.galaxy.tempXXXXX',
-		DIR      => '/tmp/',
-		UNLINK   => 1,
-		SUFFIX   => '.html'
-	);
-
-	use File::Which;
-	my $pod2md = which("pod2markdown");
-	if(! defined($pod2md)){
-		print STDERR "pod2markdown not available. Install Pod::Markdown";
-	}else{
-		my @command = ('pod2markdown',$0,$tempfile);
-		run3 \@command, \$in, \$out, \$err;
-		# Pandoc
-		my $pandoc = which("pandoc");
-		if(! defined($pandoc)){
-			print STDERR "Pandoc not available, cannot convert to RST";
-		}else{
-			@command = ("pandoc",'-f','markdown','-t','rst', $tempfile);
-			run3 \@command, \$in, \$out, \$err;
-			if(-e $tempfile){
-			    unlink($tempfile);
-			}
-			$xml_writer->characters($out);
-		}
-	}
-	$xml_writer->endTag('help');
-}
-
-no Moose;
-1;
-
-__END__
-
-=pod
-
-=encoding UTF-8
-
-=head1 NAME
-
-CPT::Galaxy
-
-=head1 VERSION
-
-version 1.99.4
-
-=head2 gen
-
-	require CPT::Galaxy;
-	my $galaxy_xml_generator = CPT::Galaxy->new();
-	$galaxy_xml_generator->gen(
-		full_options => \@options_specification,
-		appdesc      => $self->{'appdesc'},
-		appid        => $self->{'appid'},
-		appname      => $self->{'appname'},
-		defaults     => $passed_opts{'defaults'},
-		outputs      => $passed_opts{'outputs'},
-	);
-
-Generates a galaxy XML file (using XML::Writer) from the options_specification object, which is an array of 
-['file|f=s', "blah", {some_req => 'some_val'] and CPT::Parameter::* objects. For simplicity, the first type 
-is currently DEPRECATED
-
-=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