diff fastqc_site_render.R @ 0:b7c115edd970 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_site_render.R	Tue Feb 27 10:37:12 2018 -0500
@@ -0,0 +1,69 @@
+##============ 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=============================
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