diff list_render.R @ 2:391394c022b8 draft

planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/list_render.R	Sat Mar 31 21:32:17 2018 -0400
@@ -0,0 +1,38 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file(Sys.getenv('TOOL_LOG'))
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(rmarkdown)
+#------------------------------------------------
+
+#------------------------------------------------
+options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
+                                   sep = '|', header = TRUE)
+
+#------------------------------------------------
+# create three folders within working directory
+dir.create('list')
+
+#-----------------render Rmd--------------
+# copy R markdown file to working directory and render it within the working directory.
+render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list.Rmd'),
+       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
+
+# for some unknow reason, directly using REPORT as the input value for output_file parameter
+# in the render function can cause empty report file when the tool runs in batch mode.
+# the solution is to render the rmarkdown to a explicitly specified file and then copy the
+# file to ${REPORT}
+system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
+system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
+#------------------------------------------
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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