anchor.diff:  # Input data and settings
  -spectra_tar="spectra.tar";
  -db_fasta="humanprots.fasta";
  -blast_index_name="humanprots";
  -omssa_mods="mods.xml";
  -omssa_usermods="usermods.xml";
  -numthreads="4";
  +spectra_tar="spectra.tar";		# Needs to be provided (can contain mgf, mzXML, mzML, or ms2 files).
  +db_fasta="protein.fasta"; 		# Only provide the target DB (protein) in fasta format ... decoy will be created.
  +blast_index_name="prots"; 		# ignore
  +omssa_mods="mods.xml";			# File necessary for OMSSA to run.
  +omssa_usermods="usermods.xml";		# File necessary for OMSSA to run.
  +numthreads="4"; 			#ConsensusID is slow and the last process so it should run in parallel (give half of the cores to this process).
  +pmt="0.8"; 				#Precursor mass error tolerance (Daltons)
  +fmt="0.3"; 				#Fragment (Product) mass error tolerance (Daltons)
   
   
   # Convert Spectra and index databases
   spectraFiles=getSupportedSpectraFilesFromTar(spectra_tar:spectra_tar);
   mzMLFiles=convertSpectraFiles(spectraFile:spectraFiles);
  +#mzMLFiles; #Remove the hashtag at the beginning of the line to store the converted spectra.
   db_fasta_decoy=makeDecoyDB(db_fasta:db_fasta);
  -#mzMLFiles;
   db_blastDB_tar=makeBlastDB(db_fasta:db_fasta idx_name:blast_index_name);
   db_blastDB_decoy_tar=makeBlastDB(db_fasta:db_fasta_decoy idx_name:blast_index_name);
   db_msgfDB_tar=makeMsgfDB(db_fasta:db_fasta);
  
positive.code: }*
  
  # Create consensus using OpenMS ConsensusID
  deftask runConsensus(Consensus(File):idxml_results(File) numthreads) in bash *{
  	mv $idxml_results res.idXML
  	ConsensusID -in res.idXML -out cons.idXML -algorithm ranks -threads $numthreads
  	Consensus=cons.idXML
  }*
  
  
negative.code: #
  
  # Run OMSSA on the mzML data using the TOPP OMSSAAdapter
  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 res.idXML -database ${blast_index_name}.psq -omssa_executable omssacl -precursor_mass_tolerance $pmt -fragment_mass_tolerance $fmt
  	OmssaRes=res.idXML
  }*
  
  # Run MSGF+ on the mzML data using the TOPP MSGFPlusAdapter
  deftask runMsgf(MsgfRes(File):mzMLFile(File) db_fasta(File) db_msgfDB_tar(File) pmt) in bash *{
  	tar xf $db_msgfDB_tar
  	mv $mzMLFile spectra.mzML
  	mp=(`whereis MSGFPlus.jar`)
  	msgfjarpath=${mp[1]}
  	MSGFPlusAdapter -in spectra.mzML -out msgf.idXML -database $db_fasta -executable $msgfjarpath -precursor_error_units Da -precursor_mass_tolerance $pmt
  	MsgfRes=msgf.idXML
  }*
  
  # Run X!Tandem on the mzML data using the TOPP XTandenAdapter
  deftask runTandem(TandemRes(File):mzMLFile(File) db_TandemDB(File) pmt fmt) in bash *{
  	XTandemAdapter -in $mzMLFile -database $db_TandemDB -out tres.idXML -precursor_error_units Da -fragment_error_units Da -precursor_mass_tolerance $pmt -fragment_mass_tolerance $fmt
  	TandemRes=tres.idXML
  }*
  
  