Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
view collection_list_paired_render.R @ 6:a0c8b2b25774 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
author | mingchen0919 |
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date | Tue, 26 Sep 2017 13:33:22 -0400 |
parents | 66022ba24ac7 |
children |
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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) }) # 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$FORWARD_FILE_LIST = c('forward_file_list', 'L', '1', 'character') spec_list$REVERSE_FILE_LIST = c('reverse_file_list', 'R', '1', 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') ##--------2. output report and outputs -------------- spec_list$OUTPUT_HTML = c('list_paired_collection_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('list_paired_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') spec = t(as.data.frame(spec_list)) opt = getopt(spec) ##====== End of arguments handling ========== #------ Load libraries --------- library(rmarkdown) library(htmltools) library(dplyr) #----- 1. create the report directory ------------------------ system(paste0('mkdir -p ', opt$list_paired_collection_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 list_collection.Rmd ----------------------- readLines(opt$list_collection_rmd) %>% (function(x) { gsub('ECHO', opt$echo, x) }) %>% (function(x) { gsub('FORMAT', opt$format, x) }) %>% (function(x) { gsub('FORWARD_FILE_LIST', opt$forward_file_list, x) }) %>% (function(x) { gsub('REVERSE_FILE_LIST', opt$reverse_file_list, x) }) %>% (function(x) { fileConn = file('list_paired_collection.Rmd') writeLines(x, con=fileConn) close(fileConn) }) #------ 3. render all Rmd files -------- render('list_paired_collection.Rmd', output_file = opt$list_paired_collection_html) #-------4. manipulate outputs -----------------------------