gistfile1.rb

      class Trim
        include Bio::Command::Wrapper
        set_program Bio::Ngs::Utils.binary("fastx_trimmer")
        use_aliases
        add_option :first_base, :type => :numeric, :aliases => "-f", :desc => "First base to keep"
        add_option :last_base, :type => :numeric, :aliases => "-l", :desc => "Last base to keep"
        add_option :compress, :type => :boolean, :aliases => "-z", :desc => "Compress output with GZIP"
        add_option :input, :type => :string, :aliases => "-i", :desc => "Input FASTA/Q file", :collapse => true
        add_option :output, :type => :string, :aliases => "-o", :desc => "Output FASTA/Q file", :collapse => true
        add_option :trim, :type => :numeric, :aliases => "-t", :desc => "Trim N nucleotides from the end of the read"
        add_option :quality_type,  :type=>:numeric, :default => 33, :aliases => "-Q", :desc=>"Quality of fastq file"
      end