diff fastqc_site_render.R @ 7:3f92c10de274 draft

planemo upload

--- a/fastqc_site_render.R	Tue Mar 13 11:33:13 2018 -0400
+++ b/fastqc_site_render.R	Mon Apr 30 10:15:54 2018 -0400
@@ -1,84 +1,54 @@
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
 ##==============================================================
-zz = file('warnings_and_errors.txt')
+zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.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)
+
+#============== preparation ====================================
 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)
-#----------------------------------------------------
+# import libraries
+#------------------------------------------------------------------
+# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
+#------------------------------------------------------------------
+library('getopt')
+library('rmarkdown')
+library('htmltools')
 
 
-#-----------using passed arguments in R 
-#           to define system environment variables---
+# load helper functions
+source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
+# import getopt specification matrix from a csv file
+opt = getopt(getopt_specification_matrix('getopt_specification.csv', 
+                                         tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
+# define environment variables for all input values. this is useful when we 
+# want to use input values by other programming language in r markdown
 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 Rmd files =========================
+# NOTICE: 
+#       we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
+#       and render rmarkdown files in the REPORT_FILES_PATH directory.
+file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
+          to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
+system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
+# for rendering a site
+system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
 
-# copy site generating materials into OUTPUT_DIR
-dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
-system(paste0('cp -r ', TOOL_DIR, '/*.Rmd ', OUTPUT_DIR, '/site_generator/'))
-system(paste0('cp -r ', TOOL_DIR, '/_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
-system(paste0('cp -r ', TOOL_DIR, '/index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
-# render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
-render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
-# remove site generating materials from output associated directory
-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)
-#------------------------------------------
+#----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
+render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
+# add more lines below if there are more Rmd files to be rendered
 
-#-----link index.html to output-----
-cp_index = paste0('cp ', opt$X_d, '/index.html ', opt$X_o)
-system(cp_index)
-#-----------------------------------
-
-#==============the end==============
+#===============================================================
 
 
+#============== expose outputs to galaxy history ===============
+system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
+#===============================================================
 
-# 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
+##=========== End of sinking output=============================