Mercurial > repos > computational-metabolomics > mspurity_createmsp

comparison frag4feature.R @ 9:3d92b95cf6c0 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 11:38:36 +0000
parents b91b9492a4bf
children
comparison
equal deleted inserted replaced
8:b91b9492a4bf 9:3d92b95cf6c0
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