diff DESeq_results_render.R @ 3:a520a6c5e111 draft default tip

update

--- a/DESeq_results_render.R	Tue Feb 27 14:07:10 2018 -0500
+++ b/DESeq_results_render.R	Tue Feb 27 15:30:28 2018 -0500
@@ -1,105 +1,69 @@
-library(getopt)
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-library(DESeq2)
-library(pheatmap)
-library(DT)
-library(ggplot2)
-
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
 ##==============================================================
 zz = file('warnings_and_errors.txt')
 sink(zz)
 sink(zz, type = 'message')
-  ##---------below is the code for rendering .Rmd templates-----
-  
-  ##=============STEP 1: handle command line arguments==========
-  ##
-  ##============================================================
-  # 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.
-  #-------------------------------------------------------------
-  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
-  # 1. short flag alias should match the flag in the command section in the XML file.
-  # 2. long flag name can be any legal R variable names
-  # 3. two names in args_list can have common string but one name should not be a part of another name.
-  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
-  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  args_list=list()
-  ##------- 1. input data ---------------------
-  args_list$ECHO = c('echo', 'e', '1', 'character')
-  args_list$DESEQ_WORKSPACE = c('deseq_workspace', 'W', '1', 'character')
-  args_list$CONTRAST_FACTOR = c('contrast_factor', 'C', '1', 'character')
-  args_list$TREATMENT_LEVEL = c('treatment_level', 'T', '1', 'character')
-  args_list$CONDITION_LEVEL = c('condition_level', 'K', '1', 'character')
-  args_list$CLUSTERING_FACTORS = c('clustering_factors', 'M', '1', 'character')
-  ##--------2. output report and outputs --------------
-  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
-  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
-  args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
-  args_list$DESEQ_RESULTS = c('deseq_results', 'R', '1', 'character')
-  ##--------3. .Rmd templates in the tool directory ----------
-  args_list$deseq_results_RMD = c('deseq_results_rmd', 't', '1', 'character')
-  ##-----------------------------------------------------------
-  opt = getopt(t(as.data.frame(args_list)))
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+library(DESeq2)
+library(pheatmap)
+library(DT)
+library(ggplot2)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# getopt_specification_matrix(extract_short_flags('DESeq_results.xml')) %>%
+#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
 
 
-  
-  ##=======STEP 2: create report directory (optional)==========
-  ##
-  ##===========================================================
-  dir.create(opt$report_dir)
-  
-  ##=STEP 3: replace placeholders in .Rmd with argument values=
-  ##
-  ##===========================================================
-  #++ need to replace placeholders with args values one by one+
-  readLines(opt$deseq_results_rmd) %>%
-    (function(x) {
-      gsub('ECHO', opt$echo, x)
-    }) %>%
-    (function(x) {
-      gsub('DESEQ_WORKSPACE', opt$deseq_workspace, x)
-    }) %>%
-    (function(x) {
-      gsub('CONTRAST_FACTOR', opt$contrast_factor, x)
-    }) %>%
-    (function(x) {
-      gsub('TREATMENT_LEVEL', opt$treatment_level, x)
-    }) %>%
-    (function(x) {
-      gsub('CONDITION_LEVEL', opt$condition_level, x)
-    }) %>%
-    (function(x) {
-      gsub('CLUSTERING_FACTORS', opt$clustering_factors, x)
-    }) %>%
-    (function(x) {
-      gsub('REPORT_DIR', opt$report_dir, x)
-    }) %>%
-    (function(x) {
-      gsub('DESEQ_RESULTS', opt$deseq_results, x)
-    }) %>%
-    (function(x) {
-      fileConn = file('deseq_results.Rmd')
-      writeLines(x, con=fileConn)
-      close(fileConn)
-    })
-  
-
-  ##=============STEP 4: render .Rmd templates=================
-  ##
-  ##===========================================================
-  render('deseq_results.Rmd', output_file = opt$report_html)
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+              long_flags = c("X_e", "X_W", "X_C", "X_T", "X_K", "X_M", "X_o",
+                             "X_d", "X_s", "X_R", "X_t"),
+             short_flags = c("e", "W", "C", "T", "K", "M", "o", "d", "s", "R",
+                             "t"),
+     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+         data_type_flags = c("character", "character", "character", "character",
+                             "character", "character", "character",
+                             "character", "character", "character", "character")
+  )
+)
+opt = getopt(spec_matrix)
+opt
+#----------------------------------------------------
 
 
-  ##--------end of code rendering .Rmd templates----------------
+#-----------using passed arguments in R 
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+# RMD_NAME: name of Rmd file to be rendered
+# OUTPUT_REPORT: path to galaxy output report
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+RMD_NAME = 'DESeq_results.Rmd'
+OUTPUT_REPORT = opt$X_o
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
 sink()
 ##=========== End of sinking output=============================
\ No newline at end of file