Mercurial > repos > mingchen0919 > aurora_htseq
diff htseq_count_render.R @ 1:cc33706a1d4b draft
update
author | mingchen0919 |
---|---|
date | Tue, 06 Mar 2018 17:38:58 -0500 |
parents | 10a460f61ac2 |
children | db9da9716914 |
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--- a/htseq_count_render.R Tue Mar 06 15:16:40 2018 -0500 +++ b/htseq_count_render.R Tue Mar 06 17:38:58 2018 -0500 @@ -15,11 +15,23 @@ #------------get arguments into R-------------------- # library(dplyr) -# getopt_specification_matrix(extract_short_flags('')) %>% +# getopt_specification_matrix(extract_short_flags('htseq_count.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_f", "X_r", + "X_S", "X_a", "X_T", "X_i", "X_I", "X_m"), + short_flags = c("e", "o", "d", "s", "t", "f", "r", "S", "a", "T", + "i", "I", "m"), + 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) #---------------------------------------------------- @@ -32,16 +44,16 @@ #---------- 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 = 'htseq_count.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==============