Mercurial > repos > ethevenot > profia
diff profia_wrapper.R @ 2:3f8ae071bdda draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author | ethevenot |
---|---|
date | Mon, 22 Jan 2018 11:32:41 -0500 |
parents | 4753e64cf694 |
children |
line wrap: on
line diff
--- a/profia_wrapper.R Wed May 03 10:49:08 2017 -0400 +++ b/profia_wrapper.R Mon Jan 22 11:32:41 2018 -0500 @@ -95,9 +95,43 @@ cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "") -fiaset <- proFIAset(directory, - ppm = as.numeric(argVc["ppmN"]), - parallel = TRUE) +if("sizeMinN" %in% names(argVc) && argVc["sizeMinN"] != "none") { + if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") { + fiaset <- proFIAset(directory, + ppm = as.numeric(argVc["ppmN"]), + dmz = as.numeric(argVc["dmzN"]), + bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), + sizeMin = as.numeric(argVc["sizeMinN"]), + scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), + scanmax = as.numeric(argVc["scanMaxI"]), + parallel = TRUE) + } else { + fiaset <- proFIAset(directory, + ppm = as.numeric(argVc["ppmN"]), + dmz = as.numeric(argVc["dmzN"]), + bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), + sizeMin = as.numeric(argVc["sizeMinN"]), + scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), + parallel = TRUE) + } +} else { + if("scanMaxI" %in% names(argVc) && argVc["scanMaxI"] != "none") { + fiaset <- proFIAset(directory, + ppm = as.numeric(argVc["ppmN"]), + dmz = as.numeric(argVc["dmzN"]), + bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), + scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), + scanmax = as.numeric(argVc["scanMaxI"]), + parallel = TRUE) + } else { + fiaset <- proFIAset(directory, + ppm = as.numeric(argVc["ppmN"]), + dmz = as.numeric(argVc["dmzN"]), + bandCoverage = as.numeric(ifelse("bandCoverageN" %in% names(argVc), argVc["bandCoverageN"], "0.3")), + scanmin = as.numeric(ifelse("scanMinI" %in% names(argVc), argVc["scanMinI"], "1")), + parallel = TRUE) + } +} stpI <- stpI + 1 @@ -105,6 +139,7 @@ fiaset <- group.FIA(fiaset, ppmGroup = as.numeric(argVc["ppmGroupN"]), + dmz = as.numeric(argVc["dmzGroupN"]), fracGroup = as.numeric(argVc["fracGroupN"])) stpI <- stpI + 1 @@ -116,17 +151,23 @@ stpI <- stpI + 1 -kI <- as.integer(argVc["kI"]) -if(kI > 0) { +if(argVc["imputeC"] == "randomForest") { + + cat("\n", stpI, ") Imputing missing values ('impute.randomForest'):\n", sep = "") - cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "") + set.seed(123) - fiaset <- imputeMissingValues.WKNN_TN(fiaset, - k = kI) + fiaset <- impute.randomForest(fiaset, + parallel = FALSE) + + set.seed(NULL) stpI <- stpI + 1 } +###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. +###TODO add the impute.KNN_TN method + options(warn = optWrnN) @@ -205,6 +246,21 @@ cat("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "") +cat("\n\n\n============================================================================") +cat("\nAdditional information about the call:\n") +cat("\n1) Parameters:\n") +print(cbind(value = argVc)) + +cat("\n2) Session Info:\n") +sessioninfo <- sessionInfo() +cat(sessioninfo$R.version$version.string,"\n") +cat("Main packages:\n") +for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +cat("Other loaded packages:\n") +for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + +cat("============================================================================\n") + sink() rm(list = ls())