Mercurial > repos > tomnl > assess_purity_msms
changeset 10:403ef9c57550 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author | tomnl |
---|---|
date | Wed, 02 May 2018 14:26:46 -0400 |
parents | 91f38a17d82a |
children | b262a6306ffe |
files | anticipated_purity_dims.R |
diffstat | 1 files changed, 3 insertions(+), 16 deletions(-) [+] |
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--- a/anticipated_purity_dims.R Wed May 02 14:10:09 2018 -0400 +++ b/anticipated_purity_dims.R Wed May 02 14:26:46 2018 -0400 @@ -42,7 +42,7 @@ filename = sub("raw", "mzML", filename, ignore.case = TRUE) print(filename) - df <- indf[4:nrow(indf),] + df <- indf[3:nrow(indf),] if ('blank_flag' %in% colnames(df)){ df <- df[df$blank_flag==1,] } @@ -53,7 +53,7 @@ df[df$mz=='nan',]$mz <- NA } df$mz <- as.numeric(df$mz) - + mzml_file <- file.path(opt$mzML_file, filename) @@ -77,19 +77,6 @@ } -if (dir.exists(opt$mzML_file)){ - # if directory then we need to add a file name - print(filename) - if (is.na(filename)){ - print('ERROR: If a directory is provided then a filename needs to be entered - directory or automatically obtained by using a dimspy output') - quit() - }else{ - mzml_file <- file.path(opt$mzML_file, filename) - } -}else{ - mzml_file <- opt$mzML_file -} if (is.null(opt$sim)){ sim=FALSE @@ -118,7 +105,7 @@ print('FIRST ROWS OF PEAK FILE') print(head(df)) - +print(mzml_file) predicted <- msPurity::dimsPredictPuritySingle(df$mz, filepth=mzml_file, minOffset=minOffset,