comparison createDatabase.R @ 8:a507a2ccb46d draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 74e7bfbb5e70ec6e665114fa9e9863dafd7bced5

7:b663ab95274b

library(optparse)
library(xcms)
library(CAMERA)
print(sessionInfo())
print('CREATING DATABASE')



xset_pa_filename_fix <- function(opt, pa, xset){

  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables

    return(x)

  }

  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
  closeAllConnections()
  # Saves the EICS into the previously created database
  px <- msPurity::purityX(xset, saveEIC = TRUE,
                           cores=1, sqlitePth=dbPth,
                           rtrawColumns = TRUE)

}

closeAllConnections()

8:a507a2ccb46d

library(optparse)
library(xcms)
library(CAMERA)
print(sessionInfo())
print('CREATING DATABASE')

xset_pa_filename_fix <- function(opt, pa, xset){

  if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
    # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables

    return(x)

  }

  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
  
  # Saves the EICS into the previously created database
  xgroups <-  as.numeric(as.character(unique(pa@grped_df$grpid)))
  px <- msPurity::purityX(xset, 
                          saveEIC = TRUE,
                          cores=1,
                          sqlitePth=dbPth,
                          rtrawColumns = TRUE, 
                          xgroups = xgroups)

}

closeAllConnections()