diff rmarkdown_report.sh @ 0:389ef73cf4e1 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_report.sh	Fri Nov 09 11:03:16 2018 -0500
@@ -0,0 +1,28 @@
+        ######### each aurora tool generates a html file and have an files path directory associated with it.
+        mkdir -p $report.files_path &&
+
+        ######### three important paths:
+        #########   1. path to tool installation directory
+        #########   2. path to report html
+        #########   3. path to files_path directory associated with the report output.
+        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
+        export REPORT='$report' &&
+        export REPORT_FILES_PATH='$report.files_path' &&
+
+        ############ create a hidden file to store r markdown rendering log
+        touch $report.files_path/r_rendering.log.txt &&
+
+        ############ finally run the render.R script
+        Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+
+            -o $report
+            -d $report.files_path
+
+            -f $fasta_file
+            -m $masked_file
+
+            -F $ssr_fasta
+            -S $ssr_stats
+            -R $ssr_report
+
+