Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
view fastq_dump_se_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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##======= 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$FASTQ_DUMP_SE_RMD = c('fastq_dump_se_rmd', 't', '1', 'character') spec = t(as.data.frame(spec_list)) opt = getopt(spec) #------ Load libraries --------- library(rmarkdown) library(htmltools) library(dplyr) #----- 1. create the report directory ------------------------ dir.create(opt$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_se.Rmd ----------------------- readLines(opt$fastq_dump_se_rmd) %>% (function(x) { gsub('SRA_ACCESSION', opt$sra_accession, x) }) %>% (function(x) { gsub('FORMAT', opt$format, x) }) %>% (function(x) { gsub('ECHO', opt$echo, x) }) %>% (function(x) { gsub('OUTPUT_DIR', opt$output_dir, x) }) %>% (function(x) { fileConn = file('fastq_dump_se.Rmd') writeLines(x, con=fileConn) close(fileConn) }) #------ 3. render all Rmd files -------- render('fastq_dump_se.Rmd', output_file = opt$report_html) #-------4. manipulate outputs ----------------------------- sink() #/////////// END OF SINK OUTPUT ///////////////////////////