diff DESeq_render.R @ 0:6b12f3dc358a draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_render.R	Tue Feb 27 13:04:12 2018 -0500
@@ -0,0 +1,59 @@
+##============ 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')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+library(stringi)
+library(DESeq2)
+library(pheatmap)
+library(RColorBrewer)
+library(DT)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# getopt_specification_matrix(extract_short_flags('fastqc_report.xml')) %>%
+#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
+
+
+spec_matrix = as.matrix()
+opt = getopt(spec_matrix)
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R 
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+# RMD_NAME: name of Rmd file to be rendered
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+RMD_NAME = 'DESeq.Rmd'
+OUTPUT_REPORT = opt$X_o
+
+# create the output associated directory to store all outputs
+dir.create(OUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, RMD_NAME, sep = '/'), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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