Mercurial > repos > tomnl > create_sqlite_db

comparison anticipated_purity_dims.R @ 9:cc4464eb380f draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 14:33:43 -0400
parents f6996ad60d8f
children cf82f99f3638
comparison
equal deleted inserted replaced
8:f6996ad60d8f 9:cc4464eb380f
51 51
52 if ('nan' %in% df$mz){ 52 if ('nan' %in% df$mz){
53 df[df$mz=='nan',]$mz <- NA 53 df[df$mz=='nan',]$mz <- NA
54 } 54 }
55 df$mz <- as.numeric(df$mz) 55 df$mz <- as.numeric(df$mz)
56 56 mzml_file <- file.path(opt$mzML_file, filename)
57 57
58 58
59 59
60 } 60 }
61 61
75 }else{ 75 }else{
76 isotopes <- TRUE 76 isotopes <- TRUE
77 } 77 }
78 78
79 79
80 if (dir.exists(opt$mzML_file)){
81 # if directory then we need to add a file name
82 print(filename)
83 if (is.na(filename)){
84 print('ERROR: If a directory is provided then a filename needs to be entered
85 directory or automatically obtained by using a dimspy output')
86 quit()
87 }else{
88 print('filename derived from dimspy')
89 mzml_file <- file.path(opt$mzML_file, filename)
90 }
91 }else{
92 mzml_file <- opt$mzML_file
93 }
94 80
95 if (is.null(opt$sim)){ 81 if (is.null(opt$sim)){
96 sim=FALSE 82 sim=FALSE
97 }else{ 83 }else{
98 sim=TRUE 84 sim=TRUE