view combineAnnotations.R @ 4:13985cdcf0ba draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty

library(optparse)
library(msPurity)
print(sessionInfo())

# Get the parameter
option_list <- list(
  make_option(c("-s","--sm_resultPth"),type="character"),
  make_option(c("-m","--metfrag_resultPth"),type="character"),
  make_option(c("-c","--sirius_csi_resultPth"),type="character"),
  make_option(c("-p","--probmetab_resultPth"),type="character"),
  make_option(c("-sw","--sm_weight"),type="numeric"),
  make_option(c("-mw","--metfrag_weight"),type="numeric"),
  make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
  make_option(c("-pw","--probmetab_weight"),type="numeric"),
  make_option("--create_new_database", action="store_true"),
  make_option(c("-o","--outdir"),type="character", default="."),
  make_option("--eic", action="store_true")
)
opt <- parse_args(OptionParser(option_list=option_list))

print(opt)

if (!is.null(opt$create_new_database)){
  sm_resultPth <-  file.path(opt$outdir, 'combined_annotations.sqlite')
  file.copy(opt$sm_resultPth, sm_resultPth)
}else{
  sm_resultPth <- opt$sm_resultPth
}


weights <-list('sm'=opt$sm_weight,
               'metfrag'=opt$metfrag_weight,
               'sirius_csifingerid'= opt$sirius_csi_weight,
               'probmetab'=opt$probmetab_weight
               )

if (round(!sum(unlist(weights),0)==1)){

  stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
}

summary_output <- msPurity::combineAnnotations(sm_resultPth,
                             opt$metfrag_resultPth,
                             opt$sirius_csi_resultPth,
                             opt$probmetab_resultPth,
                             weights = weights)

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()