annotate createDatabase.R @ 4:3d36a391612c draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"

library(msPurity)
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
    # needs to be done due to Galaxy moving the files around and screwing up any links to files

    filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
    filepaths <- filepaths[filepaths != ""]
    new_names <- basename(filepaths)

    galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
    galaxy_names <- galaxy_names[galaxy_names != ""]

    nsave <- names(pa@fileList)
    old_filenames  <- basename(pa@fileList)
    pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
    names(pa@fileList) <- nsave

    pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
    pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
  }


 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
    if(!all(names(pa@fileList)==basename(xset@filepaths))){
       print('FILELISTS DO NOT MATCH')
       message('FILELISTS DO NOT MATCH')
       quit(status = 1)
    }else{
      xset@filepaths <- unname(pa@fileList)
    }
  }

  print(xset@phenoData)
  print(xset@filepaths)

  return(list(pa, xset))
}




option_list <- list(
  make_option(c("-o", "--outDir"), type="character"),
  make_option("--pa", type="character"),
  make_option("--xset_xa", type="character"),
  make_option("--xcms_camera_option", type="character"),
  make_option("--eic", action="store_true"),
  make_option("--cores", default=4),
  make_option("--mzML_files", type="character"),
  make_option("--galaxy_names", type="character"),
  make_option("--grpPeaklist", type="character")
)


# store options
opt<- parse_args(OptionParser(option_list=option_list))
print(opt)

loadRData <- function(rdata_path, name){
#loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() %in% name]))
}

getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet")
        return (xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
        sampclass(xset) <- xset@phenoData$sample_group
        return (xset)
    }
}


print(paste('pa', opt$pa))
print(opt$xset)

print(opt$xcms_camera_option)
# Requires
pa <- loadRData(opt$pa, 'pa')


print(pa@fileList)

# Missing list element causes failures (should be updated
# in msPurity R package for future releases)
if (!exists('allfrag', where=pa@filter_frag_params)){
    pa@filter_frag_params$allfrag <- FALSE
}

if (opt$xcms_camera_option=='xcms'){

  xset <- loadRData(opt$xset, c('xset','xdata'))
  xset <- getxcmsSetObject(xset)
  fix <- xset_pa_filename_fix(opt, pa, xset)
  pa <- fix[[1]]
  xset <- fix[[2]]
  xa <- NULL
}else{

  xa <- loadRData(opt$xset, 'xa')
  fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
  pa <- fix[[1]]
  xa@xcmsSet <- fix[[2]]
  xset <- NULL
}



if(is.null(opt$grpPeaklist)){
  grpPeaklist = NA
}else{
  grpPeaklist = opt$grpPeaklist
}



dbPth <- msPurity::createDatabase(pa,
                                   xset=xset,
                                   xsa=xa,
                                   outDir=opt$outDir,
                                   grpPeaklist=grpPeaklist,
                                   dbName='createDatabase_output.sqlite'
)





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=dbPth,
                          rtrawColumns = TRUE)

}

closeAllConnections()