Mercurial > repos > computational-metabolomics > mspurity_spectralmatching
comparison purityX.R @ 9:c33b92eeb1fb draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author | computational-metabolomics |
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date | Thu, 13 Jun 2024 11:37:41 +0000 |
parents | 77706396e7bd |
children | fcd8ef711617 |
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8:77706396e7bd | 9:c33b92eeb1fb |
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72 | 72 |
73 | 73 |
74 | 74 |
75 getxcmsSetObject <- function(xobject) { | 75 getxcmsSetObject <- function(xobject) { |
76 # XCMS 1.x | 76 # XCMS 1.x |
77 if (class(xobject) == "xcmsSet") { | 77 if (class(xobject) == "xcmsSet"){ |
78 return(xobject) | 78 return(xobject) |
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$sample_group | |
86 }else{ | |
87 xcms::sampclass(xset) <- "." | |
88 } | |
85 return(xset) | 89 return(xset) |
86 } | 90 } |
87 } | 91 } |
88 | 92 |
89 target_obj <- loadRData(opt$xset_path, opt$rdata_name) | 93 target_obj <- loadRData(opt$xset_path, opt$rdata_name) |