Mercurial > repos > galaxyp > mqppep_preproc

comparison mqppep_anova.R @ 3:bae3a23461c9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
author galaxyp
date Tue, 31 Jan 2023 22:27:00 +0000
parents b76c75521d91
children
comparison
equal deleted inserted replaced
2:a5e7469dfdfa 3:bae3a23461c9
99 c("-k", "--ksea_cutoff_statistic"), 99 c("-k", "--ksea_cutoff_statistic"),
100 action = "store", 100 action = "store",
101 default = "FDR", 101 default = "FDR",
102 type = "character", 102 type = "character",
103 help = paste0("Method for missing-value imputation,", 103 help = paste0("Method for missing-value imputation,",
104 " one of c('FDR','p.value'), but don't expect 'p.value' to work well.") 104 " one of c('FDR','p.value'), but don't expect 'p.value' to work well.")
105 ), 105 ),
106 make_option( 106 make_option(
107 c("-t", "--ksea_cutoff_threshold"), 107 c("-t", "--ksea_cutoff_threshold"),
108 action = "store", 108 action = "store",
109 default = 0.05, 109 default = 0.05,
110 type = "double", 110 type = "double",
111 help = paste0("Maximum score to be used to score a kinase enrichment as significant") 111 help = paste0(
112 "Maximum score to be used to score a kinase enrichment as significant")
112 ), 113 ),
113 make_option( 114 make_option(
114 c("-c", "--kseaMinSubstrateCount"), 115 c("-c", "--kseaMinSubstrateCount"),
115 action = "store", 116 action = "store",
116 default = "1", 117 default = "1",
267 pattern = ksea_cutoff_statistic, 268 pattern = ksea_cutoff_statistic,
268 x = c("FDR", "p.value") 269 x = c("FDR", "p.value")
269 ) 270 )
270 ) < 1 271 ) < 1
271 ) { 272 ) {
272 print(sprintf("bad ksea_cutoff_statistic argument: %s", ksea_cutoff_statistic)) 273 print(sprintf(
274 "bad ksea_cutoff_statistic argument: %s", ksea_cutoff_statistic))
273 return(-1) 275 return(-1)
274 } 276 }
275 277
276 imputation_method <- args$imputationMethod 278 imputation_method <- args$imputationMethod
277 if ( 279 if (
311 readChar(fname, limit) 313 readChar(fname, limit)
312 } else { 314 } else {
313 cat(sprintf("not a file: '%s'\n", fname)) 315 cat(sprintf("not a file: '%s'\n", fname))
314 fname 316 fname
315 } 317 }
316 #AC print(paste0("read_config_file_string: opening file '", as.character(fname), "'"))
317 # eliminate any leading whitespace 318 # eliminate any leading whitespace
318 result <- gsub("^[ \t\n]*", "", result) 319 result <- gsub("^[ \t\n]*", "", result)
319 # eliminate any trailing whitespace 320 # eliminate any trailing whitespace
320 result <- gsub("[ \t\n]*$", "", result) 321 result <- gsub("[ \t\n]*$", "", result)
321 # substitute characters escaped by Galaxy sanitizer 322 # substitute characters escaped by Galaxy sanitizer
345 cat(paste0("regex_sample_names file: ", args$regexSampleNames, "\n")) 346 cat(paste0("regex_sample_names file: ", args$regexSampleNames, "\n"))
346 regex_sample_names <- read_config_file_string(args$regexSampleNames, nc) 347 regex_sample_names <- read_config_file_string(args$regexSampleNames, nc)
347 cat(paste0("regex_sample_names: ", regex_sample_names, "\n")) 348 cat(paste0("regex_sample_names: ", regex_sample_names, "\n"))
348 349
349 if (group_filter != "none") { 350 if (group_filter != "none") {
350 cat(paste0("group_filter_patterns file: '", args$sampleGroupFilterPatterns, "'\n")) 351 cat(paste0("group_filter_patterns file: '",
351 group_filter_patterns <- read_config_file_string(args$sampleGroupFilterPatterns, nc) 352 args$sampleGroupFilterPatterns, "'\n"))
353 group_filter_patterns <-
354 read_config_file_string(args$sampleGroupFilterPatterns, nc)
352 } else { 355 } else {
353 group_filter_patterns <- ".*" 356 group_filter_patterns <- ".*"
354 } 357 }
355 cat(paste0("group_filter_patterns: ", group_filter_patterns, "\n")) 358 cat(paste0("group_filter_patterns: ", group_filter_patterns, "\n"))
356 359