Mercurial > repos > galaxyp > mqppep_preproc
comparison MaxQuantProcessingScript.R @ 1:b76c75521d91 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
| author | galaxyp |
|---|---|
| date | Fri, 28 Oct 2022 18:26:42 +0000 |
| parents | 8dfd5d2b5903 |
| children | bae3a23461c9 |
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| 0:8dfd5d2b5903 | 1:b76c75521d91 |
|---|---|
| 218 c("-e", "--enriched"), | 218 c("-e", "--enriched"), |
| 219 action = "store", | 219 action = "store", |
| 220 type = "character", | 220 type = "character", |
| 221 help = "pY or pST enriched samples (ie, 'Y' or 'ST')" | 221 help = "pY or pST enriched samples (ie, 'Y' or 'ST')" |
| 222 ) | 222 ) |
| 223 # default = "^Number of Phospho [(]STY[)]$", | |
| 224 , | 223 , |
| 225 make_option( | 224 make_option( |
| 226 c("-p", "--phosphoCol"), | 225 c("-p", "--phosphoCol"), |
| 227 action = "store", | 226 action = "store", |
| 228 type = "character", | 227 type = "character", |
| 229 help = paste0("PERL-compatible regular expression matching", | 228 help = paste0("PERL-compatible regular expression matching", |
| 230 " header of column having number of 'Phospho (STY)'") | 229 " header of column having number of 'Phospho (STY)'") |
| 231 ) | 230 ) |
| 232 # default = "^Intensity[^_]", | |
| 233 , | 231 , |
| 234 make_option( | 232 make_option( |
| 235 c("-s", "--startCol"), | 233 c("-s", "--startCol"), |
| 236 action = "store", | 234 action = "store", |
| 237 type = "character", | 235 type = "character", |
| 238 help = paste0("PERL-compatible regular expression matching", | 236 help = paste0("PERL-compatible regular expression matching", |
| 239 " header of column having first sample intensity") | 237 " header of column having first sample intensity") |
| 240 ) | 238 ) |
| 241 # default = 1, | |
| 242 , | 239 , |
| 243 make_option( | 240 make_option( |
| 244 c("-I", "--intervalCol"), | 241 c("-I", "--intervalCol"), |
| 245 action = "store", | 242 action = "store", |
| 246 type = "integer", | 243 type = "integer", |
| 247 help = paste0("Column interval between the Intensities of samples", | 244 help = paste0("Column interval between the Intensities of samples", |
| 248 " (eg, 1 if subsequent column; 2 if every other column") | 245 " (eg, 1 if subsequent column; 2 if every other column") |
| 249 ) | 246 ) |
| 250 # default = 0.75, | |
| 251 , | 247 , |
| 252 make_option( | 248 make_option( |
| 253 c("-l", "--localProbCutoff"), | 249 c("-l", "--localProbCutoff"), |
| 254 action = "store", | 250 action = "store", |
| 255 type = "double", | 251 type = "double", |
| 256 help = "Localization Probability Cutoff" | 252 help = "Localization Probability Cutoff" |
| 257 ) | 253 ) |
| 258 # default = "sum", | |
| 259 , | 254 , |
| 260 make_option( | 255 make_option( |
| 261 c("-f", "--collapse_func"), | 256 c("-f", "--collapse_func"), |
| 262 action = "store", | 257 action = "store", |
| 263 type = "character", | 258 type = "character", |
| 264 help = paste0("merge identical phosphopeptides", | 259 help = paste0("merge identical phosphopeptides", |
| 265 " by ('sum' or 'average') the intensities") | 260 " by ('sum' or 'average') the intensities") |
| 266 ) | 261 ) |
| 267 # default = "filtered_data.txt", | |
| 268 , | 262 , |
| 269 make_option( | 263 make_option( |
| 270 c("-r", "--filtered_data"), | 264 c("-r", "--filtered_data"), |
| 271 action = "store", | 265 action = "store", |
| 272 type = "character", | 266 type = "character", |
| 273 help = "filtered_data.txt" | 267 help = "filtered_data.txt" |
| 274 ) | 268 ) |
| 275 # default = "quantData.txt", | |
| 276 , | 269 , |
| 277 make_option( | 270 make_option( |
| 278 c("-q", "--quant_data"), | 271 c("-q", "--quant_data"), |
| 279 action = "store", | 272 action = "store", |
| 280 type = "character", | 273 type = "character", |