diff deseq2_render.R @ 3:caae0a188548 draft

add deseq2 package

--- a/deseq2_render.R	Thu Mar 08 20:13:30 2018 -0500
+++ b/deseq2_render.R	Thu Mar 08 21:03:01 2018 -0500
@@ -17,12 +17,25 @@
 
 
 #------------get arguments into R--------------------
-library(dplyr)
-getopt_specification_matrix(extract_short_flags('deseq2.xml')) %>%
-  write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
+# library(dplyr)
+# getopt_specification_matrix(extract_short_flags('deseq2.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_A", "X_B",
+                             "X_C", "X_D", "X_E", "X_F", "X_G", "X_H", "X_I"),
+             short_flags = c("e", "o", "d", "s", "t", "A", "B", "C", "D", "E",
+                             "F", "G", "H", "I", "J"),
+     argument_mask_flags = c(1L, 1L, 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", "character", "character")
+  )
+)
 opt = getopt(spec_matrix)
 #----------------------------------------------------
 
@@ -35,16 +48,16 @@
 #---------- 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 = 'deseq2.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, sep = '/'), output_file = OUTPUT_REPORT)
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
 #------------------------------------------
 
 #==============the end==============