| Previous changeset 0:0a2457551e25 (2017-08-07) Next changeset 2:0374e090e38e (2017-08-07) |
|
Commit message:
Uploaded |
|
added:
fastqc_report_render.R |
| b |
| diff -r 0a2457551e25 -r 22cd2369354b fastqc_report_render.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc_report_render.R Mon Aug 07 21:40:45 2017 -0400 |
| [ |
| @@ -0,0 +1,87 @@ +##======= 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) +}) + +# 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. +spec_list=list() +spec_list$READS = c('reads', 'r', '1', 'character') +spec_list$ECHO = c('echo', 'e', '1', 'character') +spec_list$FASTQC_TPL = c('fastqc_tpl', 'p', 1, 'character') +spec_list$REPORT = c('report', 'o', '1', 'character') +spec_list$REPORT_OUTPUT_DIR = c('report_output_dir', 'd', '1', 'character') + + +spec = t(as.data.frame(spec_list)) + +opt = getopt(spec) +# arguments are accessed by long flag name (the first column in the spec matrix) +# NOT by element name in the spec_list +# example: opt$help, opt$expression_file +##====== End of arguments handling ========== + + +mgsub = function(pattern, replacement, x) { + if(length(pattern) != length(replacement) ) { + stop("pattern and replacement have to be the same in length") + } + + result = x + + for(i in 1:length(pattern)) { + result = try( gsub(pattern[i], replacement[i], x = result) ) + } + + result +} + + +##====== replace variables in tpl file ====== +p = c('READS', + 'ECHO', + 'FASTQC_TPL', + 'REPORT_OUTPUT_DIR', + 'REPORT') +r = c(opt$reads, + opt$echo, + opt$fastqc_tpl, + opt$report_output_dir, + opt$report) + +fastqc_report_tpl = mgsub(p, r, readLines(opt$fastqc_tpl)) + +##====== write replaced text into Rmd file === +fileConn = file('fastqc_report.Rmd') +writeLines(fastqc_report_tpl, con=fileConn) +close(fileConn) + +##====== render Rmd files ==================== +rmarkdown::render('fastqc_report.Rmd') +file.copy('fastqc_report.html', opt$report, recursive=TRUE) +paste0('cp -r ./* ', opt$report_output_dir) %>% + system() + |