comparison biosigner_wrapper.R @ 3:fa80bd02055f draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab

2:b2414be87d4b

#!/usr/bin/env Rscript

library(batch) ## parseCommandArgs

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

tierMC <- bsnLs@tierMC

if(!is.null(tierMC)) {
    plot(bsnLs,
         tierMaxC = tierMaxC,
         file.pdfC = argVc["figure_tier"],
         .sinkC = argVc["information"])
    plot(bsnLs,
         tierMaxC = tierMaxC,
         typeC = "boxplot",
         file.pdfC = argVc["figure_boxplot"],
         .sinkC = argVc["information"])
} else {
    pdf(argVc["figure_tier"])
    plot(1, bty = "n", type = "n",
         xaxt = "n", yaxt = "n", xlab = "", ylab = "")
    text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),

tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]

if(sum(tierMC %in% tierVc)) {
    cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "")
    print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,
                 drop = FALSE])

    cat("\nAccuracy:\n")
    print(round(getAccuracyMN(bsnLs), 3))
} else
    cat("\nNo significant variable found for any classifier\n")

##--------

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

sink()

options(stringsAsFactors = strAsFacL)

rm(list = ls())

3:fa80bd02055f

#!/usr/bin/Rscript --vanilla --slave --no-site-file


library(batch) ## parseCommandArgs

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

tierMC <- bsnLs@tierMC

if(!is.null(tierMC)) {
    plot(bsnLs,
         tierMaxC = tierMaxC,
         file.pdfC = "figure_tier.pdf",
         .sinkC = argVc["information"])
    file.rename("figure_tier.pdf", argVc["figure_tier"])
    plot(bsnLs,
         tierMaxC = tierMaxC,
         typeC = "boxplot",
         file.pdfC = "figure_boxplot.pdf",
         .sinkC = argVc["information"])
    file.rename("figure_boxplot.pdf", argVc["figure_boxplot"])
} else {
    pdf(argVc["figure_tier"])
    plot(1, bty = "n", type = "n",
         xaxt = "n", yaxt = "n", xlab = "", ylab = "")
    text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),

tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]

if(sum(tierMC %in% tierVc)) {
    cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "")
    print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,
                         drop = FALSE])
    cat("\nAccuracy:\n")
    print(round(getAccuracyMN(bsnLs), 3))
} else
    cat("\nNo significant variable found for any classifier\n")

##--------

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()

options(stringsAsFactors = strAsFacL)

rm(list = ls())