Mercurial > repos > mingchen0919 > aurora_bdss_sra
changeset 3:cf17a4199861 draft
planemo upload for repository https://github.com/feltus/BDSS
author | mingchen0919 |
---|---|
date | Tue, 12 Jun 2018 09:49:08 -0400 |
parents | ad0bc5ffbd9d |
children | c062782a7534 |
files | rmarkdown_report.Rmd |
diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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) {