Mercurial > repos > tomnl > mspurity_createmsp

comparison createDatabase.R @ 2:7e7223015600 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit d9efa3f24732a92c2bcef5987289179e86d5c50f-dirty
author tomnl
date Fri, 14 Jun 2019 07:05:18 -0400
parents df2efceff4cd
children 13985cdcf0ba
comparison
equal deleted inserted replaced
1:6d1312ad450c 2:7e7223015600
66 # store options 66 # store options
67 opt<- parse_args(OptionParser(option_list=option_list)) 67 opt<- parse_args(OptionParser(option_list=option_list))
68 print(opt) 68 print(opt)
69 69
70 loadRData <- function(rdata_path, name){ 70 loadRData <- function(rdata_path, name){
71 #loads an RData file, and returns the named xset object if it is there 71 #loads an RData file, and returns the named xset object if it is there
72 load(rdata_path) 72 load(rdata_path)
73 return(get(ls()[ls() == name])) 73 return(get(ls()[ls() %in% name]))
74 } 74 }
75
76 getxcmsSetObject <- function(xobject) {
77 # XCMS 1.x
78 if (class(xobject) == "xcmsSet")
79 return (xobject)
80 # XCMS 3.x
81 if (class(xobject) == "XCMSnExp") {
82 # Get the legacy xcmsSet object
83 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
84 sampclass(xset) <- xset@phenoData$sample_group
85 return (xset)
86 }
87 }
88
75 89
76 print(paste('pa', opt$pa)) 90 print(paste('pa', opt$pa))
77 print(opt$xset) 91 print(opt$xset)
78 92
79 print(opt$xcms_camera_option) 93 print(opt$xcms_camera_option)
82 96
83 97
84 print(pa@fileList) 98 print(pa@fileList)
85 99
86 100
101
87 if (opt$xcms_camera_option=='xcms'){ 102 if (opt$xcms_camera_option=='xcms'){
88 xset <- loadRData(opt$xset, 'xset') 103
104 xset <- loadRData(opt$xset, c('xset','xdata'))
105 xset <- getxcmsSetObject(xset)
89 fix <- xset_pa_filename_fix(opt, pa, xset) 106 fix <- xset_pa_filename_fix(opt, pa, xset)
90 pa <- fix[[1]] 107 pa <- fix[[1]]
91 xset <- fix[[2]] 108 xset <- fix[[2]]
92 xa <- NULL 109 xa <- NULL
93 }else{ 110 }else{
109 126
110 127
111 128
112 dbPth <- msPurity::createDatabase(pa, 129 dbPth <- msPurity::createDatabase(pa,
113 xset=xset, 130 xset=xset,
114 # xsa=xa, 131 xsa=xa,
115 outDir=opt$outDir, 132 outDir=opt$outDir,
116 # grpPeaklist=grpPeaklist, 133 grpPeaklist=grpPeaklist,
117 dbName='createDatabase_output.sqlite' 134 dbName='createDatabase_output.sqlite'
118 ) 135 )
119 136
120 137
121 138