anchor.diff:  	ConsensusDecoyResults=runConsensus(idxml_results:MergedDecoyResults pmt:pmt numthreads:numthreads);
   
   	FDRResults=establishFDR(target_idxml:ConsensusTargetResults decoy_idxml:ConsensusDecoyResults numthreads:numthreads);
  -	idxmlResults=mapPeptides(idxml_results:FDRResults db_fasta:db_fasta);
  +	fdrResults=mapPeptides(idxml_results:FDRResults db_fasta:db_fasta);
  +
  +	protResults=inferProteins(idxml_results:fdrResults numthreads:numthreads);
  +	filteredResults=filterResults(idxml_results:protResults numthreads:numthreads);
  +	idxmlResults=filteredResults;
   }
   
   
  
positive.code: # Create consensus using OpenMS ConsensusID
  deftask runConsensus(Consensus(File):idxml_results(File) pmt numthreads) in bash *{
  	mv $idxml_results res.idXML
  	ConsensusID -in res.idXML -out cons.idXML -mz_delta $pmt -algorithm ranks -threads $numthreads
  	Consensus=cons.idXML
  }*
  
  
negative.code: #			Other Tasks
  #
  
  deftask filterResults(idxml_res(File) : idxml_results(File) numthreads) in bash *{
  	IDFilter -in $idxml_results -out $idxml_res -best:strict -unique -remove_decoys -delete_unreferenced_peptide_hits
  }*
  
  deftask inferProteins(idxml_res(File) : idxml_result(File) numthreads) in bash *{
  	ProteinInference -in $idxml_result -out $idxml_res -min_peptides_per_protein 2 -threads $numthreads
  }*
  
  # Takes decoy ConsensusID results and target ConsensusID results and performs FDR.
  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
  