annotate tool_template_render.R @ 10:49cabfe55b61 draft

update 2
author mingchen0919
date Fri, 23 Feb 2018 15:58:55 -0500
parents a9f93a4742b1
children 670e1591cc65
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
1 zz = file("warnings_and_errors.txt")
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
2 sink(zz)
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
3 sink(zz, type = "message")
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
4
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
5 # bring user inputs and command line arguments to R
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
6 spec_matrix = as.matrix(
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
7 data.frame(stringsAsFactors=FALSE,
7
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
8 long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s",
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
9 "X_t"),
6
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
10 short_flags = c("e", "A", "B", "O", "r", "d", "s", "t"),
7
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
11 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
12 data_type_flags = c("character", "character", "character", "character",
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
13 "character", "character", "character",
26a239300989 initial tool
mingchen0919
parents: 6
diff changeset
14 "character")
6
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
15 )
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
16 )
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
17 opt = getopt::getopt(spec_matrix)
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
18 opt
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
19
9
mingchen0919
parents: 8
diff changeset
20 rmarkdown::render(input = opt$X_t, output_file = opt$X_O)
6
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
21
8c3b0ffa0d14 update tool
mingchen0919
parents:
diff changeset
22 sink()