annotate sleuth.R @ 3:2c3d294dbe42 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 4adb19064a6973121680119529444286c24c1ac1

library(sleuth,
    quietly = TRUE,
    warn.conflicts = FALSE
)
library(annotables, quietly = TRUE, warn.conflicts = FALSE)
library(argparse, quietly = TRUE, warn.conflicts = FALSE)
library(tidyverse)


# 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")

################################################################################
### Input Processing
################################################################################


# Collect arguments from command line
parser <- ArgumentParser(description = "Sleuth R script")

parser$add_argument("--factorLevel", action = "append", required = FALSE)
parser$add_argument("--factorLevel_counts",
    action = "append",
    required = FALSE
)
parser$add_argument("--factorLevel_n", action = "append", required = FALSE)
parser$add_argument("--cores", type = "integer", required = FALSE)
parser$add_argument("--normalize", action = "store_true", required = FALSE)
parser$add_argument("--nbins", type = "integer", required = FALSE)
parser$add_argument("--lwr", type = "numeric", required = FALSE)
parser$add_argument("--upr", type = "numeric", required = FALSE)
parser$add_argument("--metadata_file",
    action = "append",
    required = FALSE
)
parser$add_argument("--experiment_design", required = FALSE)

args <- parser$parse_args()

if (args$experiment_design == "complex") {
    ## Complex experiment design
    ############################

    s2c <-
        read.table(
            file = args$metadata_file,
            header = TRUE,
            sep = "\t"
        )

    s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
    for (f in args$factorLevel_counts) {
        file.rename(f, paste(f, ".h5", sep = ""))
    }

    so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
    so <- sleuth_fit(so)
} else {
    ## Simple experiment design
    ###########################

    conditions <- c()
    for (x in seq_along(args$factorLevel)) {
        temp <- append(conditions, rep(args$factorLevel[[x]]))
        conditions <- temp
    }

    sample_names <-
        gsub(".fastq.+", "", basename(args$factorLevel_counts))

    design <-
        data.frame(list(
            sample = sample_names,
            condition = conditions,
            path = args$factorLevel_counts
        ))
    so <- sleuth_prep(design,
        cores = args$cores,
        normalize = args$normalize
    )
}

so <- sleuth_fit(
    so,
    ~condition,
    "full",
    n_bins = args$nbins,
    lwr = args$lwr,
    upr = args$upr
)

so <- sleuth_fit(
    so,
    ~1,
    "reduced",
    n_bins = args$nbins,
    lwr = args$lwr,
    upr = args$upr
)

so <- sleuth_lrt(so, "reduced", "full")

sleuth_table <-
    sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)

write.table(
    sleuth_table,
    file = "sleuth_table.tab",
    quote = FALSE,
    sep = "\t",
    col.names = TRUE,
    row.names = FALSE
)


outputFile <- file.path(getwd(), "pca_plot.pdf")
pdf(
    file = outputFile,
    height = 6,
    width = 9
)
plot_pca(so, color_by = "condition")
dev.off()

outputFile <- file.path(getwd(), "group_density.pdf")
pdf(
    file = outputFile,
    height = 6,
    width = 9
)
plot_group_density(
    so,
    use_filtered = TRUE,
    units = "est_counts",
    trans = "log",
    grouping = setdiff(
        colnames(so$sample_to_covariates),
        "sample"
    ),
    offset = 1
)
dev.off()