Mercurial > repos > ethevenot > profia
comparison profia_wrapper.R @ 2:3f8ae071bdda draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author | ethevenot |
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date | Mon, 22 Jan 2018 11:32:41 -0500 |
parents | 4753e64cf694 |
children |
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1:4753e64cf694 | 2:3f8ae071bdda |
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93 | 93 |
94 stpI <- 1 | 94 stpI <- 1 |
95 | 95 |
96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") | 96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") |
97 | 97 |
98 fiaset <- proFIAset(directory, | 98 if("sizeMinN" %in% names(argVc) && argVc["sizeMinN"] != "none") { |
99 ppm = as.numeric(argVc["ppmN"]), | 99 if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") { |
100 parallel = TRUE) | 100 fiaset <- proFIAset(directory, |
101 ppm = as.numeric(argVc["ppmN"]), | |
102 dmz = as.numeric(argVc["dmzN"]), | |
103 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), | |
104 sizeMin = as.numeric(argVc["sizeMinN"]), | |
105 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), | |
106 scanmax = as.numeric(argVc["scanMaxI"]), | |
107 parallel = TRUE) | |
108 } else { | |
109 fiaset <- proFIAset(directory, | |
110 ppm = as.numeric(argVc["ppmN"]), | |
111 dmz = as.numeric(argVc["dmzN"]), | |
112 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), | |
113 sizeMin = as.numeric(argVc["sizeMinN"]), | |
114 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), | |
115 parallel = TRUE) | |
116 } | |
117 } else { | |
118 if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") { | |
119 fiaset <- proFIAset(directory, | |
120 ppm = as.numeric(argVc["ppmN"]), | |
121 dmz = as.numeric(argVc["dmzN"]), | |
122 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), | |
123 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), | |
124 scanmax = as.numeric(argVc["scanMaxI"]), | |
125 parallel = TRUE) | |
126 } else { | |
127 fiaset <- proFIAset(directory, | |
128 ppm = as.numeric(argVc["ppmN"]), | |
129 dmz = as.numeric(argVc["dmzN"]), | |
130 bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), | |
131 scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), | |
132 parallel = TRUE) | |
133 } | |
134 } | |
101 | 135 |
102 stpI <- stpI + 1 | 136 stpI <- stpI + 1 |
103 | 137 |
104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "") | 138 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "") |
105 | 139 |
106 fiaset <- group.FIA(fiaset, | 140 fiaset <- group.FIA(fiaset, |
107 ppmGroup = as.numeric(argVc["ppmGroupN"]), | 141 ppmGroup = as.numeric(argVc["ppmGroupN"]), |
142 dmz = as.numeric(argVc["dmzGroupN"]), | |
108 fracGroup = as.numeric(argVc["fracGroupN"])) | 143 fracGroup = as.numeric(argVc["fracGroupN"])) |
109 | 144 |
110 stpI <- stpI + 1 | 145 stpI <- stpI + 1 |
111 | 146 |
112 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "") | 147 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "") |
114 fiaset <- makeDataMatrix(fiaset, | 149 fiaset <- makeDataMatrix(fiaset, |
115 maxo = FALSE) | 150 maxo = FALSE) |
116 | 151 |
117 stpI <- stpI + 1 | 152 stpI <- stpI + 1 |
118 | 153 |
119 kI <- as.integer(argVc["kI"]) | 154 |
120 | 155 if(argVc["imputeC"] == "randomForest") { |
121 if(kI > 0) { | 156 |
122 | 157 cat("\n", stpI, ") Imputing missing values ('impute.randomForest'):\n", sep = "") |
123 cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "") | 158 |
124 | 159 set.seed(123) |
125 fiaset <- imputeMissingValues.WKNN_TN(fiaset, | 160 |
126 k = kI) | 161 fiaset <- impute.randomForest(fiaset, |
162 parallel = FALSE) | |
163 | |
164 set.seed(NULL) | |
127 | 165 |
128 stpI <- stpI + 1 | 166 stpI <- stpI + 1 |
129 } | 167 } |
168 ###TODO Fix the error message to set 'parallel' to TRUE: You must register a 'foreach' parallel backend to run 'missForest' in parallel. Set 'parallelize' to 'no' to compute serially. | |
169 ###TODO add the impute.KNN_TN method | |
170 | |
130 | 171 |
131 options(warn = optWrnN) | 172 options(warn = optWrnN) |
132 | 173 |
133 | 174 |
134 ##------------------------------ | 175 ##------------------------------ |
203 ##-------- | 244 ##-------- |
204 | 245 |
205 cat("\nEnd of '", modNamC, "' Galaxy module call: ", | 246 cat("\nEnd of '", modNamC, "' Galaxy module call: ", |
206 as.character(Sys.time()), "\n", sep = "") | 247 as.character(Sys.time()), "\n", sep = "") |
207 | 248 |
249 cat("\n\n\n============================================================================") | |
250 cat("\nAdditional information about the call:\n") | |
251 cat("\n1) Parameters:\n") | |
252 print(cbind(value = argVc)) | |
253 | |
254 cat("\n2) Session Info:\n") | |
255 sessioninfo <- sessionInfo() | |
256 cat(sessioninfo$R.version$version.string,"\n") | |
257 cat("Main packages:\n") | |
258 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") | |
259 cat("Other loaded packages:\n") | |
260 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") | |
261 | |
262 cat("============================================================================\n") | |
263 | |
208 sink() | 264 sink() |
209 | 265 |
210 rm(list = ls()) | 266 rm(list = ls()) |