Mercurial > repos > tomnl > create_msp
changeset 1:3f1f2d545f3a draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
| author | tomnl |
|---|---|
| date | Wed, 02 May 2018 14:08:21 -0400 |
| parents | 4b417094bf71 |
| children | ac8738f96e53 |
| files | anticipated_purity_dims.R |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/anticipated_purity_dims.R Wed May 02 13:09:23 2018 -0400 +++ b/anticipated_purity_dims.R Wed May 02 14:08:21 2018 -0400 @@ -32,15 +32,16 @@ }else{ indf <- read.table(opt$peaks_file, header = TRUE, sep='\t', stringsAsFactors = FALSE) - + filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] + print(filename) # check if the data file is mzML or RAW (can only use mzML currently) so # we expect an mzML file of the same name in the same folder indf$i <- indf[,colnames(indf)==filename] indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) filename = sub("raw", "mzML", filename, ignore.case = TRUE) - + print(filename) df <- indf[4:nrow(indf),] if ('blank_flag' %in% colnames(df)){ df <- df[df$blank_flag==1,]