diff DESeq_render.R @ 0:6f94b4b9de44 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DESeq_render.R	Tue Feb 27 23:57:53 2018 -0500
@@ -0,0 +1,86 @@
+##============ 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(DESeq2)
+library(pheatmap)
+library(DT)
+library(ggplot2)
+library(genefilter)
+library(RColorBrewer)
+#------------------------------------------------
+
+
+#------------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(
+  data.frame(stringsAsFactors=FALSE,
+             long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_P", "X_N",
+                            "X_S", "X_p", "X_w"),
+             short_flags = c("e", "o", "d", "s", "t", "P", "N", "S", "p", "w"),
+             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+             data_type_flags = c("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])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_REPORT: path to galaxy output report
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+OUTPUT_REPORT = opt$X_o
+
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render site--------------
+# copy site generating materials into OUTPUT_DIR
+dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
+command_cp = paste0('cp -r ', TOOL_DIR, '/DESeq_0*.Rmd ', OUTPUT_DIR, '/site_generator')
+system(command_cp)
+system(paste0('cp -r ', TOOL_DIR, '/DESeq_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
+system(paste0('cp -r ', TOOL_DIR, '/DESeq_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
+# render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
+dir.create(paste0(OUTPUT_DIR, '/_site'))
+render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
+# remove site generating materials from output associated directory
+print(unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE))
+# move _site/* into output associated directory
+move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR)
+system(move_cmd)
+#------------------------------------------
+
+#-----link index.html to output-----
+cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT)
+system(cp_index)
+#-----------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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