Mercurial > repos > computational-metabolomics > mspurity_flagremove
comparison createDatabase.R @ 4:c635d8b0b929 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
| author | computational-metabolomics |
|---|---|
| date | Mon, 10 Aug 2020 08:31:19 -0400 |
| parents | e570f604b357 |
| children | a67b129cd78e |
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| 3:d2373ced0ded | 4:c635d8b0b929 |
|---|---|
| 92 pa <- loadRData(opt$pa, 'pa') | 92 pa <- loadRData(opt$pa, 'pa') |
| 93 | 93 |
| 94 | 94 |
| 95 print(pa@fileList) | 95 print(pa@fileList) |
| 96 | 96 |
| 97 | 97 # Missing list element causes failures (should be updated |
| 98 # in msPurity R package for future releases) | |
| 99 if (!exists('allfrag', where=pa@filter_frag_params)){ | |
| 100 pa@filter_frag_params$allfrag <- FALSE | |
| 101 } | |
| 98 | 102 |
| 99 if (opt$xcms_camera_option=='xcms'){ | 103 if (opt$xcms_camera_option=='xcms'){ |
| 100 | 104 |
| 101 xset <- loadRData(opt$xset, c('xset','xdata')) | 105 xset <- loadRData(opt$xset, c('xset','xdata')) |
| 102 xset <- getxcmsSetObject(xset) | 106 xset <- getxcmsSetObject(xset) |