Mercurial > repos > tomnl > anticipated_purity_dims
changeset 8:8bb1ce2fa184 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
| author | tomnl |
|---|---|
| date | Wed, 02 May 2018 14:15:33 -0400 |
| parents | 9d6346d2f547 |
| children | f4032a392323 |
| files | anticipated_purity_dims.R anticipated_purity_dims.xml |
| diffstat | 2 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/anticipated_purity_dims.R Wed May 02 13:22:42 2018 -0400 +++ b/anticipated_purity_dims.R Wed May 02 14:15:33 2018 -0400 @@ -32,16 +32,17 @@ }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$i <- indf[,colnames(indf)==filename] indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) filename = sub("raw", "mzML", filename, ignore.case = TRUE) - - df <- indf[4:nrow(indf),] + print(filename) + df <- indf[3:nrow(indf),] if ('blank_flag' %in% colnames(df)){ df <- df[df$blank_flag==1,] }
--- a/anticipated_purity_dims.xml Wed May 02 13:22:42 2018 -0400 +++ b/anticipated_purity_dims.xml Wed May 02 14:15:33 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="anticipated_purity_dims" name="anticipated_purity_dims" version="0.0.11"> +<tool id="anticipated_purity_dims" name="anticipated_purity_dims" version="0.0.12"> <description>Calculate the anticipated precursor ion purity from a DIMS dataset. </description> <macros>