Mercurial > repos > tomnl > dma_filelist_generation
changeset 4:dca14960284f draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
| author | tomnl |
|---|---|
| date | Thu, 03 May 2018 07:00:04 -0400 |
| parents | 19152a319f68 |
| children | baee92500726 |
| files | cameradims.R |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/cameradims.R Thu May 03 06:44:16 2018 -0400 +++ b/cameradims.R Thu May 03 07:00:04 2018 -0400 @@ -81,12 +81,16 @@ if (opt$rule_type=='extended_large'){ + + rule_sep=',' opt$rule_type <- 'user' if(opt$polarity=='pos'){ - opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) + opt$rule_path <- system.file("rules", "CAMERA_rules_PosFinal_PlusLi.csv", package = "cameraDIMS") }else{ - opt$rule_path <- read.csv(system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS"), header=TRUE) + opt$rule_path <- system.file("rules", "CAMERA_rules_NegFinal_PlusLi.csv", package = "cameraDIMS") } +}else{ + rule_sep='\t' } cameraOut <- cameraDIMS(data=df, @@ -94,7 +98,7 @@ params_adduct=paramadduct, rule_type=opt$rule_type, rule_pth=opt$rule_path, - rule_sep='\t', + rule_sep=rule_sep, rule_export=rule_export)