diff skewer_render.R @ 7:c5c297020c36 draft

planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer_render.R	Thu Apr 26 12:49:35 2018 -0400
@@ -0,0 +1,52 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt'))
+sink(zz)
+sink(zz, type = 'message')
+
+#============== preparation ====================================
+options(stringsAsFactors = FALSE)
+# import libraries
+#------------------------------------------------------------------
+# ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
+#------------------------------------------------------------------
+library('getopt')
+library('rmarkdown')
+library('htmltools')
+
+
+# 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])
+#===============================================================
+
+
+#======================== 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}')
+
+#----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
+render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/skewer.Rmd'))
+# add more lines below if there are more Rmd files to be rendered
+
+#===============================================================
+
+
+#============== expose outputs to galaxy history ===============
+system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
+#===============================================================
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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