diff fastqc_site_render.R @ 2:c64267b9f754 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty

--- a/fastqc_site_render.R	Tue Feb 27 10:40:20 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,69 +0,0 @@
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file('warnings_and_errors.txt')
-sink(zz)
-sink(zz, type = 'message')
-  
-library(getopt)
-library(rmarkdown)
-library(htmltools)
-library(plyr)
-library(dplyr)
-library(stringr)
-library(DT)
-library(reshape2)
-library(plotly)
-options(stringsAsFactors = FALSE)
-
-# getopt_specification_matrix(extract_short_flags('fastqc_report.xml')) %>%
-#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
-
-
-# get arguments into R
-spec_matrix = as.matrix(
-  data.frame(stringsAsFactors=FALSE,
-              long_flags = c("X_e", "X_r", "X_n", "X_R", "X_N", "X_c", "X_l",
-                             "X_o", "X_d", "X_s", "X_t"),
-             short_flags = c("e", "r", "n", "R", "N", "c", "l", "o", "d", "s",
-                             "t"),
-     argument_mask_flags = c(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")
-  )
-)
-opt = getopt(spec_matrix)
-
-# using passed arguments in R to define system environment variables
-do.call(Sys.setenv, opt[-1])
-
-# create the output associated directory to store all outputs
-dir.create(opt$X_d, recursive = TRUE)
-
-#-----------------render site--------------
-# copy site generating materials into folder "_site" within the output associated directory
-file.copy(opt$X_t, opt$X_d, recursive = TRUE)
-# render site to the output associated directory
-render_site(input = paste0(opt$X_d, '/aurora_fastqc_site'))
-# remove site generating materials from output associated directory
-unlink(paste0(opt$X_d, '/aurora_fastqc_site'), recursive = TRUE)
-# move _site/* into output associated directory
-move_cmd = paste0('mv ', opt$X_d, '/_site/* ', opt$X_d)
-system(move_cmd)
-#------------------------------------------
-
-#-----link index.html to output-----
-cp_index = paste0('cp ', opt$X_d, '/index.html ', opt$X_o)
-system(cp_index)
-#-----------------------------------
-
-#==============the end==============
-
-
-
-# file.copy(paste0(opt$X_d, '/index.html'), opt$X_o, recursive = TRUE)
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file