Mercurial > repos > prog > lcmsmatching
comparison search-mz @ 5:18254e8d1b72 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty
| author | prog |
|---|---|
| date | Thu, 16 Mar 2017 08:15:11 -0400 |
| parents | 1ba222315fd5 |
| children | b8f70d8216b3 |
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| 4:1ba222315fd5 | 5:18254e8d1b72 |
|---|---|
| 528 if ( ! opt[['input-col-names']][['mz']] %in% colnames(input)) | 528 if ( ! opt[['input-col-names']][['mz']] %in% colnames(input)) |
| 529 stop(paste0('No column named "', opt[['input-col-names']][['mz']], '" in input file.')) | 529 stop(paste0('No column named "', opt[['input-col-names']][['mz']], '" in input file.')) |
| 530 | 530 |
| 531 # Set columns 'all-cols' specified | 531 # Set columns 'all-cols' specified |
| 532 if ( ! is.null(opt[['all-cols']])) | 532 if ( ! is.null(opt[['all-cols']])) |
| 533 opt$rtcol <- db$getChromCol() | 533 opt$rtcol <- db$getChromCol()[['id']] |
| 534 | 534 |
| 535 # Check chrom columns | 535 # Check chrom columns |
| 536 if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) { | 536 if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) { |
| 537 dbcols <- db$getChromCol()[['id']] | 537 dbcols <- db$getChromCol()[['id']] |
| 538 unknown.cols <- opt$rtcol[ ! opt$rtcol %in% dbcols] | 538 unknown.cols <- opt$rtcol[ ! opt$rtcol %in% dbcols] |