Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
diff fastq_dump_pe_render.R @ 0:1a11c4fd13d0 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
author | mingchen0919 |
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date | Wed, 27 Sep 2017 21:41:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_dump_pe_render.R Wed Sep 27 21:41:29 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 /////////////////////////// \ No newline at end of file