anchor.diff:  
   # Index fasta database using makeblastdb from ncbi
   deftask makeBlastDB(db_blastDB_tar(File):db_fasta(File) idx_name) in bash *{
  -	makeblastdb -in $db_fasta -dbtype prot -hash_index -out $idx_name
  +	makeblastdb -in $db_fasta\
  +		-dbtype prot\
  +		-hash_index\
  +		-out $idx_name
   	tar cf db.tar --remove-files $idx_name*
   	db_blastDB_tar=db.tar
   }*
  
positive.code: #
  
  deftask filterResults(idxml_res(File) : idxml_results(File) mzMLFile(File) numthreads) in bash *{
  	bn=$(basename $mzMLFile).id_xml
  	IDFilter -in $idxml_results -out bn -best:strict -unique -remove_decoys -delete_unreferenced_peptide_hits
  	idxml_res=bn
  }*
  
  deftask inferProteins(idxml_res(File) : idxml_results(File) numthreads) in bash *{
  	ProteinInference -in $idxml_results -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
  	fdr_res=res.idXML
  }*
  
  #
  deftask mapPeptides(MappedResults(File):idxml_results(File) db_fasta(File)) in bash *{
  	PeptideIndexer -in $idxml_results -fasta $db_fasta -out mappedres.idXML -missing_decoy_action warn -allow_unmatched
  	MappedResults=mappedres.idXML
  }*
  
  # Convert resutls into easier to read csv format.
  deftask idxml2csv(csv_results(File):idxml_results(File)) in bash *{
  	res=${idxml_results}.csv
  	TextExporter -in $idxml_results -out $res
  	csv_results=$res
  }*
  
  # 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 -filter:considered_hits 5 -filter:min_support 1
  	Consensus=cons.idXML
  }*
  
  
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
  }*
  
  