# HG changeset patch
# User mingchen0919
# Date 1519400808 18000
# Node ID 8c3b0ffa0d14e23415edf42371837b38ba081494
# Parent  fc9043b919b13ef92e1df617a51bd6c9eda95ded
update tool

diff -r fc9043b919b1 -r 8c3b0ffa0d14 tool_template_render.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_template_render.R	Fri Feb 23 10:46:48 2018 -0500
@@ -0,0 +1,25 @@
+zz = file("warnings_and_errors.txt")
+sink(zz)
+sink(zz, type = "message")
+
+# bring user inputs and command line arguments to R
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+              long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s",
+                             "X_t"),
+             short_flags = c("e", "A", "B", "O", "r", "d", "s", "t"),
+     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+         data_type_flags = c("character", "character", "character", "character",
+                             "character", "character", "character",
+                             "character")
+  )
+)
+opt = getopt::getopt(spec_matrix)
+opt
+
+# build command: awk '{print $1,$2}' > output.txt and run
+X_A = paste0(paste0('$', trimws(strsplit(opt$X_A, ',')[[1]])), collapse = ',')
+extract_field_command = paste0("awk '{print ", X_A, " }' ", opt$X_B, " > ", opt$X_O)
+system(command = extract_field_command)
+
+sink()