anchor.diff:  #			Other Tasks
   #
   
  +deftask calcPEP(pepIdXML(File) : idxml_results(File)) in bash *{
  +	IDPosteriorErrorProbability -in $idxml_results\
  +		-out $pepIdXML
  +}*
  +
   deftask filterResults(idxml_res(File) : idxml_results(File) mzMLFile(File) numthreads) in bash *{
   	idxml_res=$(basename $mzMLFile).idXML
   	IDFilter -in $idxml_results\
  -		-out $idxml_res -best:strict\
  -		-unique -remove_decoys\
  -		-delete_unreferenced_peptide_hits
  +		-out $idxml_res\
  +		-best:strict\
  +		-unique\
  +		-remove_decoys\
  +		-delete_unreferenced_peptide_hits\
  +		-score:pep 0.05\
  +		-mz:unit Da
   }*
   
   deftask inferProteins(idxml_res(File) : idxml_results(File) numthreads) in bash *{
  
positive.code: 		-fasta $db_fasta\
  		-out mappedres.idXML\
  		-missing_decoy_action warn\
  		-allow_unmatched
  	MappedResults=mappedres.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_target $target_idxml\
  		-in $idxml_results\
  		-out res.idXML\
  		-threads $numthreads\
  	fdr_res=res.idXML
  }*
  
  