Mercurial > repos > mingchen0919 > one_command_liners
changeset 6:8c3b0ffa0d14 draft
update tool
| author | mingchen0919 |
|---|---|
| date | Fri, 23 Feb 2018 10:46:48 -0500 |
| parents | fc9043b919b1 |
| children | 26a239300989 |
| files | tool_template_render.R |
| diffstat | 1 files changed, 25 insertions(+), 0 deletions(-) [+] |
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--- /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()