Mercurial > repos > computational-metabolomics > mspurity_flagremove
comparison frag4feature.R @ 9:da36e8bbcfbd draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
| author | computational-metabolomics |
|---|---|
| date | Thu, 13 Jun 2024 11:35:07 +0000 |
| parents | a0ee43397d1e |
| children |
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| 8:a0ee43397d1e | 9:da36e8bbcfbd |
|---|---|
| 79 } | 79 } |
| 80 # XCMS 3.x | 80 # XCMS 3.x |
| 81 if (class(xobject) == "XCMSnExp") { | 81 if (class(xobject) == "XCMSnExp") { |
| 82 # Get the legacy xcmsSet object | 82 # Get the legacy xcmsSet object |
| 83 suppressWarnings(xset <- as(xobject, "xcmsSet")) | 83 suppressWarnings(xset <- as(xobject, "xcmsSet")) |
| 84 sampclass(xset) <- xset@phenoData$sample_group | 84 if (!is.null(xset@phenoData$sample_group)) { |
| 85 xcms::sampclass(xset) <- xset@phenoData$sample_group | |
| 86 } else { | |
| 87 xcms::sampclass(xset) <- "." | |
| 88 } | |
| 85 return(xset) | 89 return(xset) |
| 86 } | 90 } |
| 87 } | 91 } |
| 88 | 92 |
| 89 # Requires | 93 # Requires |
| 93 | 97 |
| 94 pa@cores <- opt$cores | 98 pa@cores <- opt$cores |
| 95 | 99 |
| 96 print(pa@fileList) | 100 print(pa@fileList) |
| 97 print(xset@filepaths) | 101 print(xset@filepaths) |
| 102 | |
| 98 | 103 |
| 99 if (is.null(opt$intense)) { | 104 if (is.null(opt$intense)) { |
| 100 intense <- FALSE | 105 intense <- FALSE |
| 101 } else { | 106 } else { |
| 102 intense <- TRUE | 107 intense <- TRUE |