param	value
verbose	FALSE
inputFile	../tests/testData/scaffold_tmt10plex_raw.xls
resultsFileLabel	SQ_Results
outputDir	../tests/testData/SQ_Results
proteinFastaFile	NA
scaffoldPTMSpectrumReportFile	NA
selectedProteinName	.
selectedModifName	
fdrCutoff	0.01
precursorMassFilter	NA
minNbPeptidesPerProt	1
maxNbPtmsPerPeptide	99999
minPeptideLength	1
FUniquePeptides	FALSE
ratioCutOff	1
TAdjustRatios	FALSE
normAC	.
SRawDataAnalysis	FALSE
eBayes	FALSE
SNonPairWiseStatTest	FALSE
expDesignTag	1,2,3,4:5,6,7:8,9,10
proteinQuant	TRUE
ECorrelatedSamples	FALSE
deFdrCutoff	0.01
iBAQ	FALSE
top3	FALSE
addQC	FALSE
isSaveRObject	FALSE
test	FALSE
pdfFilePath	../tests/testData/SQ_Results/SQ_Results.pdf
peptideTsvFilePath	../tests/testData/SQ_Results/SQ_Results_PEPTIDE.tsv
proteinTsvFilePath	../tests/testData/SQ_Results/SQ_Results_PROTEIN.tsv
paramsFilePath	../tests/testData/SQ_Results/SQ_Results_SQ_PARAMS.TXT
rDataFilePath	../tests/testData/SQ_Results/SQ_Results_SQ.rData
