Mercurial > repos > tomnl > create_sqlite_db

comparison anticipated_purity_dims.R @ 7:d7f4696a1f86 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 13:24:26 -0400
parents 3d8bde261c95
children f6996ad60d8f
comparison
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6:3d8bde261c95 7:d7f4696a1f86
30 df <- read.table(opt$peaks_file, header = TRUE, sep='\t') 30 df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
31 filename = NA 31 filename = NA
32 }else{ 32 }else{
33 indf <- read.table(opt$peaks_file, 33 indf <- read.table(opt$peaks_file,
34 header = TRUE, sep='\t', stringsAsFactors = FALSE) 34 header = TRUE, sep='\t', stringsAsFactors = FALSE)
35 filename = colnames(indf)[8:ncol(indf)][opt$dimspy_file_num] 35
36 filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
36 # check if the data file is mzML or RAW (can only use mzML currently) so 37 # check if the data file is mzML or RAW (can only use mzML currently) so
37 # we expect an mzML file of the same name in the same folder 38 # we expect an mzML file of the same name in the same folder
38 indf$i <- indf[,colnames(indf)==filename] 39 indf$i <- indf[,colnames(indf)==filename]
39 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) 40 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
40 41