anchor.diff:  	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);
  +	FDRResults=establishFDR(target_idxml:ConsensusTargetResults decoy_idxml:ConsensusDecoyResults numthreads:numthreads);
   	idxmlResults=mapPeptides(idxml_results:FDRResults db_fasta:db_fasta);
   }
   
  
positive.code: #
  
  # 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
  	fdr_res=res.idXML
  }*
  
  
negative.code: 	mv $mzMLFile spectra.mzML
  	mp=(`whereis MSGFPlus.jar`)
  	msgfjarpath=${mp[1]}
  	MSGFPlusAdapter -in spectra.mzML -out mres.idXML -database $db_fasta -executable $msgfjarpath -precursor_error_units Da -precursor_mass_tolerance $pmt
  	MsgfRes=mres.idXML
  }*
  
  # Run X!Tandem on the mzML data using the TOPP XTandenAdapter
  