Mercurial > repos > tomnl > mspurity_flagremove
changeset 5:1a77ed3c94b7 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 75d13d0237560528a1c6596a3ea5e327bed3e3a0
| author | tomnl |
|---|---|
| date | Tue, 18 Jun 2019 10:39:15 -0400 |
| parents | 28fb8befb3b2 |
| children | ad24f23e7d53 |
| files | combineAnnotations.R createDatabase.R |
| diffstat | 2 files changed, 1 insertions(+), 27 deletions(-) [+] |
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--- a/combineAnnotations.R Tue Jun 18 09:50:03 2019 -0400 +++ b/combineAnnotations.R Tue Jun 18 10:39:15 2019 -0400 @@ -47,32 +47,6 @@ write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) -if (!is.null(opt$eic)){ - - if (is.null(xset)){ - xset <- xa@xcmsSet - } - # previous check should have matched filelists together - xset@filepaths <- unname(pa@fileList) - - convert2Raw <- function(x, xset){ - sid <- unique(x$sample) - # for each file get list of peaks - x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])] - x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])] - x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])] - return(x) - - } - - xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset)) - - # Saves the EICS into the previously created database - px <- msPurity::purityX(xset, saveEIC = TRUE, - cores=1, sqlitePth=db_pth, - rtrawColumns = TRUE) - -} closeAllConnections()
--- a/createDatabase.R Tue Jun 18 09:50:03 2019 -0400 +++ b/createDatabase.R Tue Jun 18 10:39:15 2019 -0400 @@ -159,7 +159,7 @@ # Saves the EICS into the previously created database px <- msPurity::purityX(xset, saveEIC = TRUE, - cores=1, sqlitePth=db_pth, + cores=2, sqlitePth=dbPth, rtrawColumns = TRUE) }