diff skewer_render.R @ 1:e969699f49b6 draft

working version

--- a/skewer_render.R	Thu Mar 01 14:25:15 2018 -0500
+++ b/skewer_render.R	Fri Mar 02 09:59:25 2018 -0500
@@ -10,15 +10,28 @@
 
 library(getopt)
 library(rmarkdown)
+library(htmltools)
 #------------------------------------------------
 
 
 #------------get arguments into R--------------------
-# getopt_specification_matrix(extract_short_flags('fastqc_report.xml')) %>%
+# getopt_specification_matrix(extract_short_flags('skewer.xml')) %>%
 #   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
 
 
-spec_matrix = as.matrix()
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+              long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_X", "X_Y",
+                             "X_x", "X_y", "X_A", "X_B", "X_f", "X_r"),
+             short_flags = c("e", "o", "d", "s", "t", "X", "Y", "x", "y", "A",
+                             "B", "f", "r"),
+     argument_mask_flags = c(1L, 1L, 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",
+                             "character", "character")
+  )
+)
 opt = getopt(spec_matrix)
 #----------------------------------------------------
 
@@ -31,15 +44,17 @@
 #---------- often used variables ----------------
 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
 # TOOL_DIR: path to the tool installation directory
-OUTPUT_DIR = ''
-TOOL_DIR =   ''
-RMD_NAME = ''
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+RMD_NAME = 'skewer.Rmd'
+OUTPUT_REPORT = opt$X_o
 
 # create the output associated directory to store all outputs
-dir.create(OUT_DIR, recursive = TRUE)
-
+dir.create(OUTPUT_DIR, recursive = TRUE)
+opt
 #-----------------render Rmd--------------
-render(paste0(TOOL_DIR, RMD_NAME, sep = '/'), OUTPUT_DIR)
+paste0(TOOL_DIR, '/', RMD_NAME)
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
 #------------------------------------------
 
 #==============the end==============