Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison createDatabase.R @ 4:20768ba7f0b4 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
author computational-metabolomics
date Mon, 10 Aug 2020 08:36:22 -0400
parents d4376a743f7b
children 18c0038dde9c
comparison
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3:b800001c9f30 4:20768ba7f0b4
92 pa <- loadRData(opt$pa, 'pa') 92 pa <- loadRData(opt$pa, 'pa')
93 93
94 94
95 print(pa@fileList) 95 print(pa@fileList)
96 96
97 97 # Missing list element causes failures (should be updated
98 # in msPurity R package for future releases)
99 if (!exists('allfrag', where=pa@filter_frag_params)){
100 pa@filter_frag_params$allfrag <- FALSE
101 }
98 102
99 if (opt$xcms_camera_option=='xcms'){ 103 if (opt$xcms_camera_option=='xcms'){
100 104
101 xset <- loadRData(opt$xset, c('xset','xdata')) 105 xset <- loadRData(opt$xset, c('xset','xdata'))
102 xset <- getxcmsSetObject(xset) 106 xset <- getxcmsSetObject(xset)