anchor.diff:  #
   
   # Takes decoy ConsensusID results and target ConsensusID results and performs FDR.
  -deftask establishFDR(fdr_res(File):target_idxml(File) decoy_idxml(File)) in bash *{
  -	FalseDiscoveryRate -in_target $target_idxml -in_decoy $decoy_idxml -out res.idXML -peptides_ony
  +deftask establishFDR(fdr_res(File):target_idxml(File) decoy_idxml(File) numthreads) in bash *{
  +	FalseDiscoveryRate -in_target $target_idxml -in_decoy $decoy_idxml -out res.idXML -threads $numthreads
   	fdr_res=res.idXML
   }*
   
  
positive.code: 	ConsensusTargetResults=runConsensus(idxml_results:MergedTargetResults pmt:pmt numthreads:numthreads);
  	ConsensusDecoyResults=runConsensus(idxml_results:MergedDecoyResults pmt:pmt numthreads:numthreads);
  
  	FDRResults=establishFDR(target_idxml:ConsensusTargetResults decoy_idxml:ConsensusDecoyResults);
  	idxmlResults=mapPeptides(idxml_results:FDRResults db_fasta:db_fasta);
  }
  
  
negative.code: deftask runOmssa(OmssaRes(File):mzMLFile(File) db_blastDB_tar(File) blast_index_name pmt fmt omssa_mods(File) omssa_usermods(File)) in bash *{
  	tar xf $db_blastDB_tar
  	ln -s `which omssacl` omssacl
  	OMSSAAdapter -in $mzMLFile -out ores.idXML -database ${blast_index_name}.psq -omssa_executable omssacl -precursor_mass_tolerance $pmt -fragment_mass_tolerance $fmt
  	OmssaRes=ores.idXML
  }*
  
  # Run MSGF+ on the mzML data using the TOPP MSGFPlusAdapter
  