anchor.diff:  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
  +	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
   }*
   
   # Run MSGF+ on the mzML data using the TOPP MSGFPlusAdapter
  
positive.code: 	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
  
negative.code: 	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 numthreads:numthreads);
  	idxmlResults=mapPeptides(idxml_results:FDRResults db_fasta:db_fasta);
  }
  
  