annotate univariate_wrapper.R @ 2:09799fc16bc6 draft

planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe

#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

source_local <- function(fname){
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}

source_local("univariate_script.R")

argVc <- unlist(parseCommandArgs(evaluate=FALSE))

##------------------------------
## Initializing
##------------------------------

## options
##--------

strAsFacL <- options()$stringsAsFactors
options(stringsAsFactors = FALSE)

## packages
##---------

library(PMCMR)

## constants
##----------

modNamC <- "Univariate" ## module name

topEnvC <- environment()
flagC <- "\n"

## functions
##----------

flgF <- function(tesC,
                 envC = topEnvC,
                 txtC = NA) { ## management of warning and error messages

    tesL <- eval(parse(text = tesC), envir = envC)

    if(!tesL) {

        sink(NULL)
        stpTxtC <- ifelse(is.na(txtC),
                          paste0(tesC, " is FALSE"),
                          txtC)

        stop(stpTxtC,
             call. = FALSE)

    }

} ## flgF

## log file
##---------

sink(argVc["information"])

cat("\nStart of the '", modNamC, "' Galaxy module call: ",
    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")

## loading
##--------

datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
                                check.names = FALSE,
                                header = TRUE,
                                row.names = 1,
                                sep = "\t")))

samDF <- read.table(argVc["sampleMetadata_in"],
                    check.names = FALSE,
                    header = TRUE,
                    row.names = 1,
                    sep = "\t")

varDF <- read.table(argVc["variableMetadata_in"],
                    check.names = FALSE,
                    header = TRUE,
                    row.names = 1,
                    sep = "\t")

tesC <- argVc["tesC"]

## checking
##---------

flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")

flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata"))
flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only"))

flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes"))
flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes"))
flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only"))

flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")

flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
     txtC = "(corrected) p-value threshold must be between 0 and 1")


##------------------------------
## Computation
##------------------------------


varDF <- univariateF(datMN = datMN,
                     samDF = samDF,
                     varDF = varDF,
                     facC = argVc["facC"],
                     tesC = tesC,
                     adjC = argVc["adjC"],
                     thrN = as.numeric(argVc["thrN"]))


##------------------------------
## Ending
##------------------------------


## saving
##--------

varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
                          varDF)

write.table(varDF,
            file = argVc["variableMetadata_out"],
            quote = FALSE,
            row.names = FALSE,
            sep = "\t")

## closing
##--------

cat("\nEnd of '", modNamC, "' Galaxy module call: ",
    as.character(Sys.time()), "\n", sep = "")

sink()

options(stringsAsFactors = strAsFacL)

rm(list = ls())