comparison MaxQuantProcessingScript.R @ 1:b76c75521d91 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be

0:8dfd5d2b5903

    c("-e", "--enriched"),
    action = "store",
    type = "character",
    help = "pY or pST enriched samples (ie, 'Y' or 'ST')"
  )
  # default = "^Number of Phospho [(]STY[)]$",
  ,
  make_option(
    c("-p", "--phosphoCol"),
    action = "store",
    type = "character",
    help = paste0("PERL-compatible regular expression matching",
             " header of column having number of 'Phospho (STY)'")
  )
  # default = "^Intensity[^_]",
  ,
  make_option(
    c("-s", "--startCol"),
    action = "store",
    type = "character",
    help = paste0("PERL-compatible regular expression matching",
             " header of column having first sample intensity")
  )
  # default = 1,
  ,
  make_option(
    c("-I", "--intervalCol"),
    action = "store",
    type = "integer",
    help = paste0("Column interval between the Intensities of samples",
             " (eg, 1 if subsequent column; 2 if every other column")
  )
  # default = 0.75,
  ,
  make_option(
    c("-l", "--localProbCutoff"),
    action = "store",
    type = "double",
    help = "Localization Probability Cutoff"
  )
  # default = "sum",
  ,
  make_option(
    c("-f", "--collapse_func"),
    action = "store",
    type = "character",
    help = paste0("merge identical phosphopeptides",
             " by ('sum' or 'average') the intensities")
  )
  # default = "filtered_data.txt",
  ,
  make_option(
    c("-r", "--filtered_data"),
    action = "store",
    type = "character",
    help = "filtered_data.txt"
  )
  # default = "quantData.txt",
  ,
  make_option(
    c("-q", "--quant_data"),
    action = "store",
    type = "character",

1:b76c75521d91

    c("-e", "--enriched"),
    action = "store",
    type = "character",
    help = "pY or pST enriched samples (ie, 'Y' or 'ST')"
  )
  ,
  make_option(
    c("-p", "--phosphoCol"),
    action = "store",
    type = "character",
    help = paste0("PERL-compatible regular expression matching",
             " header of column having number of 'Phospho (STY)'")
  )
  ,
  make_option(
    c("-s", "--startCol"),
    action = "store",
    type = "character",
    help = paste0("PERL-compatible regular expression matching",
             " header of column having first sample intensity")
  )
  ,
  make_option(
    c("-I", "--intervalCol"),
    action = "store",
    type = "integer",
    help = paste0("Column interval between the Intensities of samples",
             " (eg, 1 if subsequent column; 2 if every other column")
  )
  ,
  make_option(
    c("-l", "--localProbCutoff"),
    action = "store",
    type = "double",
    help = "Localization Probability Cutoff"
  )
  ,
  make_option(
    c("-f", "--collapse_func"),
    action = "store",
    type = "character",
    help = paste0("merge identical phosphopeptides",
             " by ('sum' or 'average') the intensities")
  )
  ,
  make_option(
    c("-r", "--filtered_data"),
    action = "store",
    type = "character",
    help = "filtered_data.txt"
  )
  ,
  make_option(
    c("-q", "--quant_data"),
    action = "store",
    type = "character",