anchor.diff:  	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
  +	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
   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
  +	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
   }*
   
  
positive.code: 
  # 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
  	tar cf db.tar --remove-files $idx_name*
  	db_blastDB_tar=db.tar
  }*
  
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
  }*
  
  