anchor.diff:  		-fasta $db_fasta\
   		-out mappedres.idXML\
   		-missing_decoy_action warn\
  -		-allow_unmatched
  +		-allow_unmatched\
  +		-aaa_max 4\
  +		-enzyme:name Trypsin\
  +		-enzyme:specificity semi
   	MappedResults=mappedres.idXML
   }*
   
  
positive.code: #			Other Tasks
  #
  
  deftask filterResults(idxml_res(File) : idxml_results(File) mzMLFile(File) numthreads) in bash *{
  	idxml_res=$(basename $mzMLFile).idXML
  	IDFilter -in $idxml_results\
  		-out $idxml_res -best:strict\
  		-unique -remove_decoys\
  		-delete_unreferenced_peptide_hits
  }*
  
  deftask inferProteins(idxml_res(File) : idxml_results(File) numthreads) in bash *{
  
negative.code: }*
  
  # Create consensus using OpenMS ConsensusID
  deftask runConsensus(Consensus(File):idxml_results(File) pmt fmt numthreads) in bash *{
  	mv $idxml_results res.idXML
  	ConsensusID -in res.idXML\
  		-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
  }*
  
  