diff fastqc_site_render.R @ 0:d732d4526c6d draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_site_render.R	Tue Aug 08 10:14:46 2017 -0400
@@ -0,0 +1,196 @@
+##======= 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$READS = c('reads', 'r', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$FASTQC_SITE = c('fastqc_site', 'o', '1', 'character')
+spec_list$FASTQC_SITE_DIR = c('fastqc_site_dir', 'd', '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$x01 = c('x01_evaluation_overview', 'p', '1', 'character')
+    spec_list$x02 = c('x02_fastqc_original_reports', 'a', '1', 'character')
+    spec_list$x1 = c('x1_per_base_quality_scores', 'b', '1', 'character')
+    spec_list$x2 = c('x2_per_base_N_content', 'c', '1', 'character')
+    spec_list$x3 = c('x3_per_sequence_quality_scores', 'f', '1', 'character')
+    spec_list$x4 = c('x4_per_sequence_GC_content', 'g', '1', 'character')
+    spec_list$x5 = c('x5_per_base_sequence_content', 'h', '1', 'character')
+
+##------------------------------------------------------------------
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(plyr)
+library(stringr)
+library(dplyr)
+library(highcharter)
+library(DT)
+library(reshape2)
+library(Kmisc)
+library(plotly)
+library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$fastqc_site_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.
+
+
+    #----- Copy index.Rmd and _site.yml files to job working direcotry -----
+    file.copy(opt$index_rmd, 'index.Rmd', recursive=TRUE)
+    file.copy(opt$site_yml, '_site.yml', recursive=TRUE)
+    #---------------------------------------------------------
+    
+    #----- 01_evaluation_overview.Rmd -----------------------
+    readLines(opt$x01_evaluation_overview) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        gsub('READS', opt$reads, x)
+      }) %>%
+      (function(x) {
+        gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('01_evaluation_overview.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 1_per_base_quality_scores.Rmd --------------------
+    readLines(opt$x1_per_base_quality_scores) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('1_per_base_quality_scores.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 2_per_base_N_content.Rmd -------------------------
+    readLines(opt$x2_per_base_N_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('2_per_base_N_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 3_per_sequence_quality_scores.Rmd ----------------
+    readLines(opt$x3_per_sequence_quality_scores) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('3_per_sequence_quality_scores.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    
+    #----- 4_per_sequence_GC_content.Rmd --------------------
+    readLines(opt$x4_per_sequence_GC_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('4_per_sequence_GC_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    
+    #----- 5_per_base_sequence_content.Rmd ------------------
+    readLines(opt$x5_per_base_sequence_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('5_per_base_sequence_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+
+    #----- 02_fastqc_original_reports.Rmd -------------------
+    readLines(opt$x02_fastqc_original_reports) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('02_fastqc_original_reports.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+
+
+
+#------ 3. render all Rmd files with render_site() --------
+render_site()    
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy index.html to the report output path
+#   b. copy all files in 'my_site' to the report output directory
+file.copy('my_site/index.html', opt$fastqc_site, recursive=TRUE)
+paste0('cp -r my_site/* ', opt$fastqc_site_dir) %>%
+  system()
+
+