annotate frag4feature.R @ 0:35898942bfbb draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"

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

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


  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)])
  }
  print(pa@fileList)

  if(!is.null(xset)){

    print(xset@filepaths)

    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)
       }
   }
 }

  return(list(pa, xset))
}


option_list <- list(
  make_option(c("-o", "--out_dir"), type="character"),
  make_option("--pa", type="character"),
  make_option("--xset", type="character"),
  make_option("--ppm", default=10),
  make_option("--plim", default=0.0),
  make_option("--convert2RawRT", action="store_true"),
  make_option("--intense", action="store_true"),
  make_option("--createDB", action="store_true"),
  make_option("--cores", default=4),
  make_option("--mzML_files", type="character"),
  make_option("--galaxy_names", type="character"),
  make_option("--grp_peaklist", type="character"),
  make_option("--useGroup", action="store_true")
)

# 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]))
}

# This function retrieve a xset like object
#@author Gildas Le Corguille [e-mail]
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)
    }
}

# Requires
pa <- loadRData(opt$pa, 'pa')
xset <- loadRData(opt$xset, c('xset','xdata'))
xset <- getxcmsSetObject(xset)

pa@cores <- opt$cores

print(pa@fileList)
print(xset@filepaths)

if(is.null(opt$intense)){
  intense = FALSE
}else{
  intense = TRUE
}

if(is.null(opt$convert2RawRT)){
    convert2RawRT = FALSE
}else{
    convert2RawRT= TRUE
}

if(is.null(opt$createDB)){
    createDB = FALSE
}else{
    createDB = TRUE
}

if(is.null(opt$useGroup)){
    fix <- xset_pa_filename_fix(opt, pa, xset)
    pa <- fix[[1]]
    xset <- fix[[2]]
    useGroup=FALSE
}else{
    # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object
    print('useGroup')
    fix <- xset_pa_filename_fix(opt, pa)
    pa <- fix[[1]]
    useGroup=TRUE
}


if(is.null(opt$grp_peaklist)){
    grp_peaklist = NA
}else{
    grp_peaklist = opt$grp_peaklist
}
print(useGroup)



pa <- msPurity::frag4feature(pa=pa,
                             xset=xset,
                             ppm=opt$ppm,
                             plim=opt$plim,
                             intense=intense,
                             convert2RawRT=convert2RawRT,
                             db_name='alldata.sqlite',
                             out_dir=opt$out_dir,
                             grp_peaklist=grp_peaklist,
                             create_db=createDB,
                             use_group=useGroup)

print(pa)
save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData'))

pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])

print(head(pa@grped_df))
write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t')