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#!/usr/bin/env perl
# PODNAME: leel.pl
# ABSTRACT: The Elite of the Phylogenomic Back-Translators

use Modern::Perl '2011';

use Getopt::Euclid qw(:vars);

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV_verbosity
        ? join q{ }, map { '#' x (2 + $_) } 1..$ARGV_verbosity
        : q{}
    ;
}
## use critic

use Smart::Comments -ENV;
use Config::Any;

use aliased 'Bio::MUST::Apps::Leel';

# read configuration file
my $config = Config::Any->load_files( {
    files           => [ $ARGV_config ],
    flatten_to_hash => 1,
    use_ext         => 1,
} );

# build leel object
# Note: default args are propagated to all orgs
my $leel = Leel->new(
    config  => $config->{$ARGV_config},
    infiles => \@ARGV_infiles,
);

# use leel as factory for run_proc object
# Note: CLI parameters are introduced here
my %args;
$args{debug_mode} = $ARGV_verbosity > 5 ? 1 : 0;
$args{out_dir}    = $ARGV_outdir if $ARGV_outdir;
$args{threads}    = $ARGV_threads;
my $rp = $leel->run_proc(\%args);

__END__

=pod

=head1 NAME

leel.pl - The Elite of the Phylogenomic Back-Translators

=head1 VERSION

version 0.213470

=head1 USAGE

    leel.pl <infiles> --config=<file> [optional arguments]

=head1 REQUIRED ARGUMENTS

=over

=item <infiles>