Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
changeset 20:531c00a2acbf draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b3bd3152ad843fa878cb043b8abb88397ddbba4e-dirty
| author | mingchen0919 |
|---|---|
| date | Sat, 14 Oct 2017 17:15:39 -0400 |
| parents | 14a50f9cca69 |
| children | a709a705ce09 |
| files | bdss_client_render.R bdss_client_sra_pe_render.R bdss_client_sra_se_render.R |
| diffstat | 3 files changed, 30 insertions(+), 30 deletions(-) [+] |
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--- 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)
--- 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)
--- 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)