Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
view mirdeep2_mapper_render.R @ 4:543ee6fdadeb draft default tip
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 15:06:46 -0400 |
parents | 963905bcb754 |
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. spec_list=list() ##------- 1. input data --------------------- spec_list$FASTQ_READS = c('reads', 'r', '1', 'character') spec_list$REFERENCE_GENOME = c('reference_genome', 'g', 1, 'character') spec_list$ECHO = c('echo', 'e', '1', 'character') ##--------2. output report and report site directory -------------- spec_list$OUTPUT_HTML = c('mirdeep2_mapper', 'o', '1', 'character') spec_list$OUTPUT_DIR = c('mirdeep2_mapper_dir', 'd', '1', 'character') spec_list$READS_COLLAPSED = c('reads_collapsed', 'm', '1', 'character') spec_list$READ_X_COLLAPSED_VS_GENOME = c('reads_collapsed_vs_genome', 'n', '1', 'character') spec_list$REPORT_LOG = c("report_log", 't', '1', 'character') ##---------other parameters--------------- spec_list$PARSE_TO_FASTA = c('parse_to_fasta', 'b', '1', 'character') spec_list$CLEAN_ENTRIES = c('clean_entries', 'c', '1', 'character') spec_list$CLIP_3_ADAPTER = c('clip_3_adapter', 'f', '2', 'character') spec_list$DISCARD_SHORTER_READS = c('discard_shorter_reads', 'h', '1', 'character') spec_list$COLLAPSE_READS_OR_NOT = c('collapse_reads_or_not', 'j', '1', 'character') spec_list$MAP_WITH_ONE_MISMATCH = c('map_with_one_mismatch', 'k', '1', 'character') spec_list$MAP_UP_TO_POSITION = c('map_up_to_position', 'l', '1', 'character') ##--------3. Rmd templates sitting in the tool directory ---------- ## _site.yml and index.Rmd files spec_list$SITE_YML = c('site_yml', 's', 1, 'character') spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character') ## other Rmd body template files spec_list$MIRDEEP2_MAPPER_RMD = c('mirdeep2_mapper_rmd', 'p', '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 ========== #------ Load libraries --------- library(rmarkdown) library(plyr) # library(stringr) library(dplyr) # library(highcharter) # library(DT) # library(reshape2) # library(plotly) # library(formattable) library(htmltools) #----- 1. create the report directory ------------------------ paste0('mkdir -p ', opt$mirdeep2_mapper_dir) %>% system() #----- 2. generate Rmd files with Rmd templates -------------- # a. templates without placeholder variables: # copy templates from tool directory to the working directory. # b. templates with placeholder variables: # substitute variables with user input values and place them in the working directory. #----- mirdeep2_mapper.Rmd ----------------------- readLines(opt$mirdeep2_mapper_rmd) %>% (function(x) { gsub('ECHO', opt$echo, x) }) %>% (function(x) { gsub('FASTQ_READS', opt$reads, x) }) %>% (function(x) { gsub('REFERENCE_GENOME', opt$reference_genome, x) }) %>% (function(x) { gsub('PARSE_TO_FASTA', opt$parse_to_fasta, x) }) %>% (function(x) { gsub('CLEAN_ENTRIES', opt$clean_entries, x) }) %>% (function(x) { gsub('CLIP_3_ADAPTER', opt$clip_3_adapter, x) }) %>% (function(x) { gsub('DISCARD_SHORTER_READS', opt$discard_shorter_reads, x) }) %>% (function(x) { gsub('COLLAPSE_READS', opt$collapse_reads, x) }) %>% (function(x) { gsub('MAP_WITH_ONE_MISMATCH', opt$map_with_one_mismatch, x) }) %>% (function(x) { gsub('MAP_UP_TO_POSITION', opt$map_up_to_position, x) }) %>% (function(x) { gsub('OUTPUT_DIR', opt$mirdeep2_mapper_dir, x) }) %>% (function(x) { fileConn = file('mirdeep2_mapper.Rmd') writeLines(x, con=fileConn) close(fileConn) }) #------ 3. render all Rmd files with render() -------- render('mirdeep2_mapper.Rmd', output_file = opt$mirdeep2_mapper) #-------4. manipulate outputs ----------------------------- # a. copy non-site files file.copy('reads_collapsed.fa', opt$reads_collapsed, recursive=TRUE) file.copy('reads_collapsed_vs_genome.arf', opt$reads_collapsed_vs_genome, recursive=TRUE) file.copy('report.log', opt$report_log, recursive=TRUE)