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lib/BioX/Map/CLIS/Cmd/MapCompare.pm  view on Meta::CPAN

package BioX::Map::CLIS::Cmd::MapCompare;
use Modern::Perl;
use IO::All;
use Carp "confess";
use Moo;
use MooX::Options prefer_commandline => 1, with_config_from_file => 1;
use MooX::Cmd;
use BioX::Map;
use Types::Standard qw(Int Str Bool Enum);

our $VERSION = '0.0.12'; # VERSION:
# ABSTRACT: a wrapper for mapping software


around _build_config_identifier => sub { 'berry' };
around _build_config_prefix => sub { 'biox_map' };



option indir => (
  is        => 'ro',
  format    => 's',
  short     => 'i',
  default   => '',
  doc       => "path of indir include fastq files",
);


option outdir => (
  is        => 'ro',
  format    => 's',
  short     => 'o',
  doc       => "path of output dir include mapping result",
  default   => './',
);


option summary_file => (
  is        => 'ro',
  format    => 's',
  short     => 's',
  doc       => 'path of summary file',
  default   => "summary.txt",
);


option process_tool => (
  is        => 'ro',
  format    => 'i',
  short     => 'p',
  doc       => "cpu number used by soap or bwa",
  default   => 1,
);


option process_sample => (
  is        => 'ro',
  format    => 'i',
  short     => 'P',
  doc       => "number of samples running parallel",
  default   => 1,
);