Mercurial > repos > eschen42 > mqppep_anova

comparison mqppep_anova.R @ 15:2c5f1a2fe16a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
author eschen42
date Sat, 26 Mar 2022 02:27:12 +0000
parents b41a077af3aa
children 61adb8801b73
comparison
equal deleted inserted replaced
14:6679616d0c18 15:2c5f1a2fe16a
30 " path to text file having one column and no header") 30 " path to text file having one column and no header")
31 ), 31 ),
32 make_option( 32 make_option(
33 c("-f", "--firstDataColumn"), 33 c("-f", "--firstDataColumn"),
34 action = "store", 34 action = "store",
35 default = "10", 35 default = "^Intensity[^_]",
36 type = "character", 36 type = "character",
37 help = "First column of intensity values" 37 help = "First column of intensity values"
38 ), 38 ),
39 make_option( 39 make_option(
40 c("-m", "--imputationMethod"), 40 c("-m", "--imputationMethod"),
108 # Check parameter values 108 # Check parameter values
109 109
110 if (! file.exists(args$inputFile)) { 110 if (! file.exists(args$inputFile)) {
111 stop((paste("Input file", args$inputFile, "does not exist"))) 111 stop((paste("Input file", args$inputFile, "does not exist")))
112 } 112 }
113 input_file <- args$inputFile 113 input_file <- args$inputFile
114 alpha_file <- args$alphaFile 114 alpha_file <- args$alphaFile
115 first_data_column <- args$firstDataColumn 115 imputed_data_file_name <- args$imputedDataFile
116 imp_qn_lt_data_filenm <- args$imputedQNLTDataFile
117 report_file_name <- args$reportFile
118
116 imputation_method <- args$imputationMethod 119 imputation_method <- args$imputationMethod
117 print( 120 print(
118 grepl( 121 grepl(
119 pattern = imputation_method, 122 pattern = imputation_method,
120 x = c("group-median", "median", "mean", "random") 123 x = c("group-median", "median", "mean", "random")
131 ) { 134 ) {
132 print(sprintf("bad imputationMethod argument: %s", imputation_method)) 135 print(sprintf("bad imputationMethod argument: %s", imputation_method))
133 return(-1) 136 return(-1)
134 } 137 }
135 138
139 # read with default values, when applicable
136 mean_percentile <- args$meanPercentile 140 mean_percentile <- args$meanPercentile
137 print("mean_percentile is:") 141 sd_percentile <- args$sdPercentile
138 cat(str(mean_percentile)) 142 # in the case of 'random" these values are ignored by the client script
139 143 if (imputation_method == "random") {
140 sd_percentile <- args$sdPercentile 144 print("mean_percentile is:")
141 print("sd_percentile is:") 145 cat(str(mean_percentile))
142 cat(str(mean_percentile)) 146
143 147 print("sd_percentile is:")
144 148 cat(str(mean_percentile))
145 regex_sample_names <- gsub("^[ \t\n]*", "", 149 }
146 readChar(args$regexSampleNames, 1000) 150
147 ) 151 # convert string parameters that are passed in via config files:
148 regex_sample_names <- gsub("[ \t\n]*$", "", 152 # - firstDataColumn
149 regex_sample_names 153 # - regexSampleNames
150 ) 154 # - regexSampleGrouping
151 cat(regex_sample_names) 155 read_config_file_string <- function(fname, limit) {
152 cat("\n") 156 # eliminate any leading whitespace
153 157 result <- gsub("^[ \t\n]*", "", readChar(fname, limit))
154 regex_sample_grouping <- gsub("^[ \t\n]*", "", 158 # eliminate any trailing whitespace
155 readChar(args$regexSampleGrouping, 1000) 159 result <- gsub("[ \t\n]*$", "", result)
156 ) 160 # substitute characters escaped by Galaxy sanitizer
157 regex_sample_grouping <- gsub("[ \t\n]*$", "", 161 result <- gsub("__lt__", "<", result)
158 regex_sample_grouping 162 result <- gsub("__le__", "<=", result)
159 ) 163 result <- gsub("__eq__", "==", result)
160 cat(regex_sample_grouping) 164 result <- gsub("__ne__", "!=", result)
161 cat("\n") 165 result <- gsub("__gt__", ">", result)
162 166 result <- gsub("__ge__", ">=", result)
163 imputed_data_file_name <- args$imputedDataFile 167 result <- gsub("__sq__", "'", result)
164 imp_qn_lt_data_filenm <- args$imputedQNLTDataFile 168 result <- gsub("__dq__", '"', result)
165 report_file_name <- args$reportFile 169 result <- gsub("__ob__", "[", result)
166 170 result <- gsub("__cb__", "]", result)
167 print("regex_sample_names is:") 171 }
168 cat(str(regex_sample_names)) 172 cat(paste0("first_data_column file: ", args$firstDataColumn, "\n"))
169 173 cat(paste0("regex_sample_names file: ", args$regexSampleNames, "\n"))
170 print("regex_sample_grouping is:") 174 cat(paste0("regex_sample_grouping file: ", args$regexSampleGrouping, "\n"))
171 cat(str(regex_sample_grouping)) 175 nc <- 1000
176 regex_sample_names <- read_config_file_string(args$regexSampleNames, nc)
177 regex_sample_grouping <- read_config_file_string(args$regexSampleGrouping, nc)
178 first_data_column <- read_config_file_string(args$firstDataColumn, nc)
179 cat(paste0("first_data_column: ", first_data_column, "\n"))
180 cat(paste0("regex_sample_names: ", regex_sample_names, "\n"))
181 cat(paste0("regex_sample_grouping: ", regex_sample_grouping, "\n"))
172 182
173 # from: https://github.com/molgenis/molgenis-pipelines/wiki/ 183 # from: https://github.com/molgenis/molgenis-pipelines/wiki/
174 # How-to-source-another_file.R-from-within-your-R-script 184 # How-to-source-another_file.R-from-within-your-R-script
175 # Function location_of_this_script returns the location of this .R script 185 # Function location_of_this_script returns the location of this .R script
176 # (may be needed to source other files in same dir) 186 # (may be needed to source other files in same dir)