#!/usr/bin/Rscript
"usage: performDE.R [options]

options:
--bamfiles=<file> bamfiles
--design=<file> design data frame
--gtffile=<file> gene feature file
--format=<string> pdf or html. [default: html]
" -> doc

library("docopt")
opts <- docopt(doc)

.design <- opts$design
if(is.null(.design))
    .design <- system.file("extdata/sample_table.csv", package="airway")

.bamfiles <- opts$bamfiles
if(is.null(.bamfiles)){
    .bamfiles <- list.files(system.file("extdata", package="airway"), "*.bam",
                            full.names = TRUE)
}else{
    .bamfiles <- strsplit(opts$bamfiles, ",")[[1]]
}

.gtffile <- opts$gtffile
if(is.null(.gtffile))
    .gtffile <- system.file("extdata/Homo_sapiens.GRCh37.75_subset.gtf",
                            package="airway")
## create param list
lst <- list(design = normalizePath(.design),
            gtffile = normalizePath(.gtffile),
            bamfiles = normalizePath(.bamfiles),
            currentPath = normalizePath("."))


## render the report
.format <- switch(opts$format,
                  "pdf" = "pdf_document",
                  "html" = "html_document",
                  {"pdf_document"})

rmarkdown::render("/report/rnaseqGene.Rmd", .format,
                  output_dir = ".",
                  params = lst)

# For rabix execution in the cloud,
# this is now a workaround to move intermediate files
