Mercurial > repos > computational-metabolomics > mspurity_puritya

comparison purityX.R @ 9:10e56e53668c draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:41:39 +0000
parents 33d733850e85
children 50abb1833b42
comparison
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8:33d733850e85 9:10e56e53668c
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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)