diff bdss_client_sra_pe_render.R @ 0:614e9553f366 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bdss_client_sra_pe_render.R	Tue Oct 10 20:19:52 2017 -0400
@@ -0,0 +1,96 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+        error=function(){
+          cat(geterrmessage(), file=stderr())
+          quit("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")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(getopt)
+  library(tools)
+})
+
+#/////////////////////// SINK WARNINGS AND ERRORS TO A FILE FOR DEBUGGING ///////////
+zz = file('warnings_and_errors.txt')
+sink(zz)
+sink(zz, type = 'message')
+
+# column 1: the long flag name
+# column 2: the short flag alias. A SINGLE character string
+# column 3: argument mask
+#           0: no argument
+#           1: argument required
+#           2: argument is optional
+# column 4: date type to which the flag's argument shall be cast.
+#           possible values: logical, integer, double, complex, character.
+##------- 1. input data ---------------------
+spec_list=list()
+spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
+spec_list$FORMAT = c('format', 'f', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+##--------2. output report and outputs --------------
+spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
+spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
+spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
+##--------3. Rmd templates in the tool directory ----------
+spec_list$FASTQ_DUMP_PE_RMD = c('fastq_dump_pe_rmd', 't', '1', 'character')
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+
+#----- 1. create the report directory ------------------------
+dir.create(opt$output_dir)
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+#----- 01 fastq_dump_pe.Rmd -----------------------
+readLines(opt$fastq_dump_pe_rmd) %>%
+  (function(x) {
+    gsub('SRA_ACCESSION', opt$sra_accession, x)
+  }) %>%
+  (function(x) {
+    gsub('FORMAT', opt$format, x)
+  }) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$output_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('fastq_dump_pe.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+#------ 3. render all Rmd files --------
+render('fastq_dump_pe.Rmd', output_file = opt$report_html)
+
+
+#-------4. manipulate outputs -----------------------------
+
+
+
+
+
+sink()
+#/////////// END OF SINK OUTPUT ///////////////////////////
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