Mercurial > repos > tomnl > assess_purity_msms
changeset 2:146699c00d38 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
| author | tomnl |
|---|---|
| date | Tue, 27 Mar 2018 11:49:44 -0400 |
| parents | c694d8172abf |
| children | 51baec6406f5 |
| files | anticipated_purity_dims.R anticipated_purity_lcms.R assess_purity_msms.R create_sqlite_db.R frag4feature.R spectral_matching.R track_rt_raw.R |
| diffstat | 7 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/anticipated_purity_dims.R Tue Mar 27 05:41:35 2018 -0400 +++ b/anticipated_purity_dims.R Tue Mar 27 11:49:44 2018 -0400 @@ -1,5 +1,6 @@ library(msPurity) library(optparse) +print(sessionInfo()) option_list <- list( make_option(c("--mzML_file"), type="character"),
--- a/anticipated_purity_lcms.R Tue Mar 27 05:41:35 2018 -0400 +++ b/anticipated_purity_lcms.R Tue Mar 27 11:49:44 2018 -0400 @@ -1,5 +1,6 @@ library(msPurity) library(optparse) +print(sessionInfo()) option_list <- list( make_option(c("--xset_path"), type="character"),
--- a/assess_purity_msms.R Tue Mar 27 05:41:35 2018 -0400 +++ b/assess_purity_msms.R Tue Mar 27 11:49:44 2018 -0400 @@ -1,5 +1,6 @@ library(msPurity) library(optparse) +print(sessionInfo()) option_list <- list( make_option(c("-o", "--out_dir"), type="character"),
--- a/create_sqlite_db.R Tue Mar 27 05:41:35 2018 -0400 +++ b/create_sqlite_db.R Tue Mar 27 11:49:44 2018 -0400 @@ -2,6 +2,7 @@ library(optparse) library(xcms) library(CAMERA) +print(sessionInfo()) print('CREATING DATABASE')
--- a/frag4feature.R Tue Mar 27 05:41:35 2018 -0400 +++ b/frag4feature.R Tue Mar 27 11:49:44 2018 -0400 @@ -1,6 +1,7 @@ library(optparse) library(msPurity) library(xcms) +print(sessionInfo()) xset_pa_filename_fix <- function(opt, pa, xset){
--- a/spectral_matching.R Tue Mar 27 05:41:35 2018 -0400 +++ b/spectral_matching.R Tue Mar 27 11:49:44 2018 -0400 @@ -1,5 +1,7 @@ library(msPurity) library(optparse) +print(sessionInfo()) + option_list <- list( make_option(c("-o", "--out_dir"), type="character"), @@ -92,4 +94,4 @@ print(cmd) scan_hits <- DBI::dbGetQuery(con, cmd) -write.table(scan_hits, file.path(opt$out_dir, 'scan_hits.tsv'), row.names=FALSE, sep='\t') \ No newline at end of file +write.table(scan_hits, file.path(opt$out_dir, 'scan_hits.tsv'), row.names=FALSE, sep='\t')