new_contents: # ----------------------------------------------------------------------------
  # Copyright (c) 2015--, micronota development team.
  #
  # Distributed under the terms of the Modified BSD License.
  #
  # The full license is in the file COPYING.txt, distributed with this software.
  # ----------------------------------------------------------------------------
  
  from os import makedirs
  from os.path import join
  
  from burrito.parameters import FlagParameter, ValuedParameter
  from burrito.util import CommandLineApplication, ResultPath
  
  
  class _DiamondCommon(CommandLineApplication):
      pass
  
  
  class DiamondMakeDB(CommandLineApplication):
      _command = 'diamond makedb'
      _parameters = {
          '--in': ValuedParameter(
              Prefix='--', Name='in', Delimiter=' ', IsPath=True),
          '--db': ValuedParameter(
              Prefix='--', Name='db', Delimiter=' ', IsPath=True),
          '--block-size': ValuedParameter(
              Prefix='--', Name='block-size', Delimiter=' '),
          '--threads': ValuedParameter(
              Prefix='--', Name='threads', Delimiter=' ')}
      _suppress_stderr = False
  
      def _accept_exit_status(self, exit_status):
          return exit_status == 0
  
      pass
  
  
  class _DiamondBlastpx(CommandLineApplication):
      _valued_nonpath_options = [
          # -p max Number of CPU threads.
          '--threads',
          # -d Path to DIAMOND database file
          '--db',
          # -q Path to query input file in FASTA or FASTQ format
          # (may be gzip compressed).
          '--query',
          # -a
          '--daa',
          # 11 Gap open penalty.
          '--gapopen',
          # 1 Gap extension penalty.
          '--gapextend',
          # BLOSUM62 Scoring matrix.
          '--matrix',
          # Enable SEG masking of low complexity segments in the query (yes/no).
          # The default is no for blastp and yes for blastx.
          '--seg',
          # -k 25 The maximum number of target sequences per query to
          # keep alignments for.
          '--max-target-seqs',
          # Keep alignments within the given percentage range of the top
          # alignment score for a query (overrides –max-target-seqs option).
          '--top',
          # -e 0.001 Maximum expected value to keep an alignment.
          '--evalue',
          # Minimum bit score to keep an alignment. Setting this option
          # will override the --evalue parameter.
          '--min-score']
      pass
  
  
  class DiamondBlastp(CommandLineApplication):
      _command = 'diamond blastp'
  
      pass
  
subject: Add diamond wrappers