# ##############################################
#    Please fill these blanks after the colon.
# ##############################################
# Make sure all space are replaced by dot(.). For example, 
# Average Intensity Ratio is replaced by Average.Intensity.Ratio.
#
# The location of the files generated from the Columbus system
        datapath : 
# The location of output files 
         outpath :
# The control well ID. 
# Leave case.wells as blank will include all wells except positive & negative 
# control and neglect.well. Please write in one line seperated by comma (,).
positive.control :
negative.control :
    neglect.well :
       case.well :
# The location of the well-gene specification file (.csv (comma separator)). 
# Make sure the first row is the colum names, eg. Barcode, Well, GeneSymbol
         genemap : 
# The organism
        organism : 
# The location of the file name specification file (.csv (comma separator)). 
# Leave it blank if you have a consistent report format and file name format.
        platemap :
# The format of the files, Matrix or Tab (Table format)
      cellformat : 
#
# ###########################################
#    Please check these paramters
# ###########################################
#
# An example of the file name. For example, if your file names 
# for.example_0205-s2-1.txt means the experiment is performed on plate 1, 
# and it is the second replicate, the barcode showed on the well-gene 
# specification file is DSIHGA01, the paramters are as follows.
   eg.filename : for.example_0205-s2-1.txt
        rep.id : s2
        exp.id : 1
           sep : -
       barcode : DSIHGA01
# In the well-gene specification file, if the well ID is B1, B2, ..., B11, 
# the well.digits = 1; while B01, B02, ..., B11, the well.digits = 2; 
# and B001, B002, ..., B011, the well.digits = 3.
   well.digits : 2
# Analyze items. For example: Average.Intensity.of.Nuclei. 
# We add a new item Average.Total.Intensity if you are interested in the total 
# intensity from both the nucleus and the cytoplasm.
# Please write in one line seperated by comma (,).
     cellnames : Average.Intensity.of.Nuclei, Average.Intensity.of.Cytoplasm, Average.Total.Intensity, Average.Intensity.Ratio
# Normalization method MP, PMed, Z, Ctr, None
   norm.method : MP
# Quality control method plateCorrelation, wellSd, zFactor, cellNumber
    opm.qcType : plateCorrelation, wellSd, zFactor, cellNumber
# Quality control threshold
 correlationTh : 0.8
     zfactorTh : 0.5
  cellnumberTh : 50
if.replace.badPlateData : TRUE
# Hit detection method stable, ksd, kmsd
    sig.method : stable
 sig.threshold : 0.05
sig.pvalue.threshold : 0.05
# Require a detailed report or only the selected hit list
       verbose : TRUE
# The report file name
   summaryFile : summary.txt
# The report of gene enrichment analysis
  functionFile : functions.txt