Mercurial > repos > tomnl > anticipated_purity_dims
changeset 9:f4032a392323 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author | tomnl |
---|---|
date | Wed, 02 May 2018 14:31:57 -0400 |
parents | 8bb1ce2fa184 |
children | 9849786c1f50 |
files | anticipated_purity_dims.R anticipated_purity_dims.xml |
diffstat | 2 files changed, 3 insertions(+), 16 deletions(-) [+] |
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--- a/anticipated_purity_dims.R Wed May 02 14:15:33 2018 -0400 +++ b/anticipated_purity_dims.R Wed May 02 14:31:57 2018 -0400 @@ -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,
--- a/anticipated_purity_dims.xml Wed May 02 14:15:33 2018 -0400 +++ b/anticipated_purity_dims.xml Wed May 02 14:31:57 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="anticipated_purity_dims" name="anticipated_purity_dims" version="0.0.12"> +<tool id="anticipated_purity_dims" name="anticipated_purity_dims" version="0.0.13"> <description>Calculate the anticipated precursor ion purity from a DIMS dataset. </description> <macros>