# HG changeset patch
# User mingchen0919
# Date 1507746979 14400
# Node ID c0b8476fbc85c55e35b2e43f26a397a664669b53
# Parent  03893b1ee3ef032589f38c48bbfef8e0bb447e28
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

diff -r 03893b1ee3ef -r c0b8476fbc85 bdss_client.Rmd
--- a/bdss_client.Rmd	Wed Oct 11 14:04:57 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 14:36:19 2017 -0400
@@ -29,7 +29,7 @@
 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
 ```
 
-# Download and extract reads
+# Download data
 
 ```{r 'download and extract reads'}
 # create a directory to store read files
@@ -40,18 +40,8 @@
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
     bdss_command = paste0('cd ./read_files_directory && /tool_deps/_conda/bin/bdss transfer -u ', url)
-    system(bdss_command)
+    print(system(bdss_command, intern = TRUE))
 }
 ```
 
-* `fastq-dump` command
-```{r}
-print(command)
-```
 
-* `command line stdout`
-
-```{r}
-system(command = command, intern = TRUE)
-```
-