# HG changeset patch
# User mingchen0919
# Date 1528811348 14400
# Node ID cf17a419986122c5b5dcf528b3c76486c056ddce
# Parent  ad0bc5ffbd9d4d0c2ff280ec95ff1f9c0e80b1da
planemo upload for repository https://github.com/feltus/BDSS

diff -r ad0bc5ffbd9d -r cf17a4199861 rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Tue Jun 12 09:43:17 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 09:49:08 2018 -0400
@@ -65,7 +65,7 @@
 Sys.setenv(PATH=paste0('/main/sites/galaxy/galaxy/tools/_conda/bin:', Sys.getenv('PATH')))
 
 # download and extract reads (single end)
-sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
+sra_ids_se = strsplit(gsub(',', ' ', opt$X_s), ' ')[[1]]
 sra_ids_se = sra_ids_se[sra_ids_se != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_ids_se) {
@@ -89,7 +89,7 @@
 }
 
 # download and extract reads (paired end)
-sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
+sra_ids_pe = strsplit(gsub(',', ' ', opt$X_p), ' ')[[1]]
 sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_ids_pe) {