diff sleuth.R @ 3:172091d47f5a draft default tip

planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sleuth.R	Tue Jun 12 17:58:47 2018 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env Rscript
+
+# A command-line interface to sleuth for use with Galaxy This script modified
+# from https://github.com/pachterlab/bears_analyses/blob/master/sleuth.R
+# https://github.com/nturaga/bioc-galaxy-integration/blob/master/README.md
+
+## Command to run tool:
+## Rscript sleuth.R --indir test-rscript --metadata test-rscript/metadata.txt
+## --full_model '~condition' --reduced_model '~1'
+## --gene_anno_name 'hsapiens_gene_ensembl'
+
+# 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")
+
+library("getopt")
+library("tools")
+options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+# get options, using the spec as defined by the enclosed list.
+spec <- matrix(c(
+  "quiet",          "q", 0, "logical",
+  "help",           "h", 0, "logical",
+  "indir",          "i", 1, "character",
+  "metadata",       "m", 1, "character",
+  "full_model",     "f", 1, "character",
+  "reduced_model",  "r", 1, "character",
+  "gene_anno_name", "a", 2, "character"),
+  byrow = TRUE, ncol = 4)
+opt <- getopt(spec)
+
+# if help was asked for print a friendly message and exit with a non-zero error
+# code
+if (!is.null(opt$help)) {
+  cat(getopt(spec, usage = TRUE))
+  q(status = 1)
+}
+
+# enforce the following required arguments
+if (is.null(opt$indir)) {
+  cat("'indir' is required\n")
+  q(status = 1)
+}
+if (is.null(opt$metadata)) {
+  cat("'metadata' is required\n")
+  q(status = 1)
+}
+if (is.null(opt$full_model)) {
+  cat("'full_model' is required\n")
+  q(status = 1)
+}
+if (is.null(opt$reduced_model)) {
+  cat("'reduced_model' is required\n")
+  q(status = 1)
+}
+
+verbose <- if (is.null(opt$quiet)) {
+  TRUE
+} else {
+  FALSE
+}
+
+suppressPackageStartupMessages({
+  library("sleuth")
+  library("biomaRt")
+})
+
+s2c <- read.table(file.path(opt$metadata), header = TRUE, stringsAsFactors = FALSE)
+run_dirs <- s2c$sample
+kal_dirs <- c()
+
+for (dir in run_dirs) {
+  kal_dirs <- c(kal_dirs, file.path(opt$indir, dir, "kallisto"))
+}
+
+s2c <- dplyr::mutate(s2c, path = kal_dirs)
+
+if (!is.null(opt$gene_anno_name)) {
+  mart <- biomaRt::useMart(biomart = "ensembl", dataset = opt$gene_anno_name)
+  t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
+    "external_gene_name"), mart = mart)
+  t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id,
+    ext_gene = external_gene_name)
+  so <- sleuth_prep(s2c, as.formula(opt$full_model), target_mapping = t2g, read_bootstrap_tpm = TRUE,
+    extra_bootstrap_summary = TRUE)
+} else {
+  so <- sleuth_prep(s2c, as.formula(opt$full_model), read_bootstrap_tpm = TRUE,
+    extra_bootstrap_summary = TRUE)
+}
+so <- sleuth_fit(so, as.formula(opt$full_model), "full")
+so <- sleuth_fit(so, as.formula(opt$reduced_model), "reduced")
+so <- sleuth_lrt(so, "reduced", "full")
+sleuth_deploy(so, opt$indir)
+
+cat("Successfully finished script.\n")