anchor.diff:  }*
   
   deftask makeDecoyDB(db_fasta_decoy(File):db_fasta(File)) in bash *{
  -	DecoyDatabase -in $db_fasta\
  -		-out decoy.fasta\
  -		-append
  +	DecoyDatabase -in $db_fasta -out decoy.fasta
   	db_fasta_decoy=decoy.fasta
   }*
  -
  -deftask appendDecoyDB(db_fasta(File):db_fasta(File)) in bash *{
  -	DecoyDatabase -in $db_fasta\
  -		-out decoy.fasta\
  -		-append
  -	db_fasta=decoy.fasta
  -}*
  
positive.code: 		-out cons.idXML\
  		-rt_delta 5\
  		-mz_delta $pmt\
  		-algorithm PEPMatrix\
  		-threads $numthreads\
  		-filter:considered_hits 10\
  		-filter:min_support 0\
  		-min_shared 2\
  		-mass_tolerance $fmt
  	Consensus=cons.idXML
  }*
  
  
negative.code: 	FalseDiscoveryRate -in_target $target_idxml\
  		-in_decoy $decoy_idxml\
  		-out res.idXML\
  		-threads $numthreads
  	fdr_res=res.idXML
  }*
  deftask calculateFDR(fdr_res(File):idxml_results(File) numthreads) in bash *{
  	FalseDiscoveryRate -in $idxml_results\
  		-out res.idXML\
  		-threads $numthreads
  	fdr_res=res.idXML
  }*
  
  