Phenyx engine usage

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Phenyx usage

phenyx-dbsearch --help
Allowed options:
  -h [ --help ]                produce help message!
  -v [ --version ]             print executable version
  -f [ --fullversion ]         print executable full klist of versions
  --phenyxconfig arg           set config (phenyx.conf) file
  --config arg                 set the search parameter config xml file 
  --identification-job arg     set the xml file containing the ms/ms spectra
  --peptspectraid arg          idi
  --samplefilter arg           set the filter on wich sample are used (format 
                               is 'spectrumType=msms;instrument=QTOF;digested_y
                               n=yes')
  --database arg               list of databases
  --dbblockaclist arg          directory where to find files with dbblock root 
                               and .aclist.txt suffix (to limit the search to 
                               the given list of ac per block) WARNING: if 
                               stated, must have the same number as --database
  --insilicodef arg            file with the defintion of all modres, enzymes, 
                               elements etc. for the user, and the group she 
                               belongs to
  --nbrndpep arg               number of random peptides to compute random 
                               score distribution
  --recordbestpeptmatches      record best peptide match per spectrum
  --bestpeptperspectrum arg    keep only the best peptide match per spectrum
  --returnaconly               return matched AC's (separated by ':' on the 
                               first line + a bit more info
  --writepmscoringdetails      write peptide matches Olav scoring details
  --saveselectepeptmatches arg write the selected_peptmatches_AUTO.xml
  --savespectrainfo arg        write spectra info (score distribution...) into 
                               xml file
  --loadSpectraInfo arg        read spectra info from file
  --savepackedspectra arg      save packed spectra into a binary file
  --savesampledscores          saves sample score in MsCompoundInfo
  --loadpackedspectra arg      read packed msms data from file (faster reading,
                               no parsing)
  --xmloutputversion arg       xml version for output
  --stdout arg                 redirect sdtout towards a file (for master node)
  --stderr arg                 redirect sdterr towards a file
  --resultsummary arg          one line summary text
  --exitonerrorfile arg        writes file with xml error details if exec has 
                               crashed
  --webseye arg                set a webseye file
  --compression arg            set compression level
  --filter arg                 filters