R/convert_files.R

In wilsontom/msconverteR: Convert vendor specific mass spectrometry files to mzML

#' Covert Files
#'
#' Convert vendor specific mass spectrometry files to the open `.mzML` format. This functions makes a `system` call to `docker` in order to convert files.
#' Conversion arguments should be supplied to the `args` parameter exactly as they would be for `msconvert` but omitting the `--filter` prefix.
#'
#' For example to convert a file with vendor specific centroiding only;
#'
#' `convert_files(rawFiles, outpath = NULL, msconvert_args = 'peakPicking true 1-')`
#'
#' To only retain positive mode data;
#'
#' `convert_files(rawFiles, outpath = NULL, msconvert_args = c('peakPicking true 1-', 'polarity positive'))`
#'
#'
#' @param files the absolute filepath vendor specific files to be converted
#' @param outpath an optional filepath where `.mzML` files will be saved to. If `NULL` then `.mzML` files are saved to the same location as input files.
#' @param msconvert_args a character vector of arguments to pass to `msconvert`.
#' @param docker_args additional arguments to pass to `docker run`
#' @export

convert_files <-
  function(files,
           outpath = NULL,
           msconvert_args = c(),
           docker_args = c())
  {
    mount_point <- stringr::str_remove(files[1],
                                       paste0('/',
                                              basename(files[1])))

    mount_point <- normalizePath(mount_point)

    if (is.null(outpath)) {
      mount_out <- mount_point
    } else{
      mount_out <- normalizePath(outpath)
    }

    docker_args <- paste(docker_args, collapse = ' ')
    docker_run <-
      paste('docker run --rm -e WINEDEBUG=-all', docker_args, '-v ')


    DOCKER_CMD_A <-
      paste0(
        docker_run,
        mount_point,
        ':/data',
        ' -v ',
        mount_out,
        ':/outpath ',
        'chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert '
      )

    if (length(msconvert_args) > 0) {
      ArgumentDictionary <- c(
        'peakPicking true 1-',
        'polarity positive',
        'polarity negative',
        'msLevel 1',
        'msLevel 2',
        'msLevel 3'

      )

      DictMat <- match(msconvert_args, ArgumentDictionary)

      if (any(is.na(DictMat)) == TRUE) {
        stop('Invalid msconvert arguments. Check documentation and try again',
             call. = FALSE)
      }

      command_args <- lapply(msconvert_args, function(x) {
        paste0('--filter ', '"', x, '"')
      })
    } else {
      command_args <- list()
    }


    command_args <-
      paste0(' --ignoreUnknownInstrumentError  --mzML ', do.call('paste', command_args))

    if (is.null(outpath)) {
      for (i in seq_along(files)) {
        DOCKER_RUN <-
          paste0(DOCKER_CMD_A, '/data/',
                 basename(files[i]),
                 command_args)
        system(DOCKER_RUN, intern = FALSE)
      }
    } else{
      for (i in seq_along(files)) {
        DOCKER_RUN <-
          paste0(DOCKER_CMD_A,
                 '/data/',
                 basename(files[i]),
                 command_args,
                 '  -o /outpath/')
        system(DOCKER_RUN, intern = FALSE)
      }
    }

    return(invisible(NULL))
  }