# HG changeset patch
# User mingchen0919
# Date 1508015739 14400
# Node ID 531c00a2acbf48f7b403a268cfc7bd4126cd2d4a
# Parent  14a50f9cca69680eb003de84042fda73ddaca86d
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty

diff -r 14a50f9cca69 -r 531c00a2acbf bdss_client_render.R
--- a/bdss_client_render.R	Sat Oct 14 15:36:30 2017 -0400
+++ b/bdss_client_render.R	Sat Oct 14 17:15:39 2017 -0400
@@ -1,3 +1,10 @@
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+library(RCurl)
+
+
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
 ##==============================================================
@@ -37,20 +44,13 @@
   
   opt = getopt(t(as.data.frame(args_list)))
   
-  ##=============STEP 2: loading libraries=====================
-  ##
-  ##===========================================================
-  library(rmarkdown)
-  library(htmltools)
-  library(dplyr)
-  library(RCurl)
   
-  ##=======STEP 3: create report directory (optional)==========
+  ##=======STEP 2: create report directory (optional)==========
   ##
   ##===========================================================
   dir.create(opt$report_dir)
   
-  ##=STEP 4: replace placeholders in .Rmd with argument values=
+  ##=STEP 3: replace placeholders in .Rmd with argument values=
   ##
   ##===========================================================
   #++ need to replace placeholders with args values one by one+
@@ -71,7 +71,7 @@
       close(fileConn)
     })
   
-  ##=============STEP 5: render .Rmd templates=================
+  ##=============STEP 4: render .Rmd templates=================
   ##
   ##===========================================================
   render('bdss_client.Rmd', output_file = opt$report_html)
diff -r 14a50f9cca69 -r 531c00a2acbf bdss_client_sra_pe_render.R
--- a/bdss_client_sra_pe_render.R	Sat Oct 14 15:36:30 2017 -0400
+++ b/bdss_client_sra_pe_render.R	Sat Oct 14 17:15:39 2017 -0400
@@ -1,3 +1,10 @@
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+library(RCurl)
+
+
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
 ##==============================================================
@@ -39,20 +46,13 @@
   
   opt = getopt(t(as.data.frame(args_list)))
   
-  ##=============STEP 2: loading libraries=====================
-  ##
-  ##===========================================================
-  library(rmarkdown)
-  library(htmltools)
-  library(dplyr)
-  library(RCurl)
   
-  ##=======STEP 3: create report directory (optional)==========
+  ##=======STEP 2: create report directory (optional)==========
   ##
   ##===========================================================
   dir.create(opt$report_dir)
   
-  ##=STEP 4: replace placeholders in .Rmd with argument values=
+  ##=STEP 3: replace placeholders in .Rmd with argument values=
   ##
   ##===========================================================
   #++ need to replace placeholders with args values one by one+
@@ -79,7 +79,7 @@
       close(fileConn)
     })
   
-  ##=============STEP 5: render .Rmd templates=================
+  ##=============STEP 4: render .Rmd templates=================
   ##
   ##===========================================================
   render('bdss_client_sra_se.Rmd', output_file = opt$report_html)
diff -r 14a50f9cca69 -r 531c00a2acbf bdss_client_sra_se_render.R
--- a/bdss_client_sra_se_render.R	Sat Oct 14 15:36:30 2017 -0400
+++ b/bdss_client_sra_se_render.R	Sat Oct 14 17:15:39 2017 -0400
@@ -1,3 +1,10 @@
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+library(dplyr)
+library(RCurl)
+
+
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
 ##==============================================================
@@ -39,20 +46,13 @@
   
   opt = getopt(t(as.data.frame(args_list)))
   
-  ##=============STEP 2: loading libraries=====================
-  ##
-  ##===========================================================
-  library(rmarkdown)
-  library(htmltools)
-  library(dplyr)
-  library(RCurl)
   
-  ##=======STEP 3: create report directory (optional)==========
+  ##=======STEP 2: create report directory (optional)==========
   ##
   ##===========================================================
   dir.create(opt$report_dir)
   
-  ##=STEP 4: replace placeholders in .Rmd with argument values=
+  ##=STEP 3: replace placeholders in .Rmd with argument values=
   ##
   ##===========================================================
   #++ need to replace placeholders with args values one by one+
@@ -79,7 +79,7 @@
       close(fileConn)
     })
   
-  ##=============STEP 5: render .Rmd templates=================
+  ##=============STEP 4: render .Rmd templates=================
   ##
   ##===========================================================
   render('bdss_client_sra_se.Rmd', output_file = opt$report_html)