comparison anticipated_purity_dims.R @ 6:3d8bde261c95 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80

5:9ab472c5714c

    isotopes <- FALSE
}else{
    isotopes <- TRUE
}

print('FIRST ROWS OF PEAK FILE')
print(head(df))

if (dir.exists(opt$mzML_file)){
  # if directory then we need to add a file name
  print(filename)
  if (is.na(filename)){

}else if (opt$iwNorm=='QE5'){
    iwNorm = TRUE
    iwNormFun = msPurity::iwNormQE.5()
}


predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                     filepth=mzml_file,
                                     minOffset=minOffset,
                                     maxOffset=maxOffset,

                                     iwNorm = iwNorm,
                                     iwNormFun = iwNormFun
                                     )
predicted <- cbind(df, predicted)


write.table(predicted, file.path(opt$out_dir, 'anticipated_dims_purity.tsv'), row.names=FALSE, sep='\t')

6:3d8bde261c95

    isotopes <- FALSE
}else{
    isotopes <- TRUE
}


if (dir.exists(opt$mzML_file)){
  # if directory then we need to add a file name
  print(filename)
  if (is.na(filename)){

}else if (opt$iwNorm=='QE5'){
    iwNorm = TRUE
    iwNormFun = msPurity::iwNormQE.5()
}

print('FIRST ROWS OF PEAK FILE')
print(head(df))

predicted <- msPurity::dimsPredictPuritySingle(df$mz,
                                     filepth=mzml_file,
                                     minOffset=minOffset,
                                     maxOffset=maxOffset,

                                     iwNorm = iwNorm,
                                     iwNormFun = iwNormFun
                                     )
predicted <- cbind(df, predicted)

print(head(predicted))
print(file.path(opt$out_dir, 'anticipated_purity_dims.tsv'))
write.table(predicted, file.path(opt$out_dir, 'anticipated_purity_dims.tsv'), row.names=FALSE, sep='\t')