comparison edger.R @ 12:a8305cf0c951 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc

11:f2843df56434

# Record starting time
time_start <- as.character(Sys.time())

# setup R error handling to go to stderr
options(show.error.messages = F, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, F)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

    if (file == "") {
      file <- stdout()
    } else if (substring(file, 1L, 1L) == "|") {
      file <- pipe(substring(file, 2L), "w")
      on.exit(close(file))
    }
    else {
      file <- file(file, ifelse(append, "a", "w"))
      on.exit(close(file))
    }
  }
  .Internal(cat(list(...), file, sep, fill, labels, append))

byrow = TRUE, ncol = 4
)
opt <- getopt(spec)


if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
  cat("A counts matrix (or a set of counts files) is required.\n")
  q(status = 1)
}

if (is.null(opt$cpmReq)) {

postfilter_count <- nrow(data$counts)
filtered_count <- prefilter_count - postfilter_count

# Name rows of factors according to their sample
row.names(factors) <- names(data$counts)
factor_list <- sapply(names(factors), paste_listname)

# Generating the DGEList object "data"
samplenames <- colnames(data$counts)
genes <- data$genes
data <- DGEList(data$counts)

for (i in seq_along(factor_list)) {
  formula <- paste(formula, factor_list[i], sep = "+")
}

formula <- formula(formula)
design <- model.matrix(formula)

for (i in seq_along(factor_list)) {
  colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
}

12:a8305cf0c951

# Record starting time
time_start <- as.character(Sys.time())

# setup R error handling to go to stderr
options(show.error.messages = FALSE, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, FALSE)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

    if (file == "") {
      file <- stdout()
    } else if (substring(file, 1L, 1L) == "|") {
      file <- pipe(substring(file, 2L), "w")
      on.exit(close(file))
    } else {
      file <- file(file, ifelse(append, "a", "w"))
      on.exit(close(file))
    }
  }
  .Internal(cat(list(...), file, sep, fill, labels, append))

byrow = TRUE, ncol = 4
)
opt <- getopt(spec)


if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
  cat("A counts matrix (or a set of counts files) is required.\n")
  q(status = 1)
}

if (is.null(opt$cpmReq)) {

postfilter_count <- nrow(data$counts)
filtered_count <- prefilter_count - postfilter_count

# Name rows of factors according to their sample
row.names(factors) <- names(data$counts)
factor_list <- names(factors)

# Generating the DGEList object "data"
samplenames <- colnames(data$counts)
genes <- data$genes
data <- DGEList(data$counts)

for (i in seq_along(factor_list)) {
  formula <- paste(formula, factor_list[i], sep = "+")
}

formula <- formula(formula)
design <- model.matrix(formula, factors)

for (i in seq_along(factor_list)) {
  colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
}