R/cmd-kraken2-tools.R

In blit: Bioinformatics Library for Integrated Tools

#' KrakenTools is a suite of scripts to be used alongside the Kraken,
#' KrakenUniq, Kraken 2, or Bracken programs.
#'
#' @description These scripts are designed to help Kraken users with downstream
#' analysis of Kraken results.
#'
#' @param script Name of the kraken2 script. One of
#' `r oxford_comma(code_quote(KrakenToolsScripts))`.
#' @param ... `r rd_dots("kraken_tools")`.
#' @inheritParams python
#' @seealso 
#' - <https://github.com/jenniferlu717/KrakenTools>
#' 
#' `r rd_seealso()`
#' @inherit exec return
#' @family command
#' @export
kraken_tools <- make_command(
    "kraken_tools",
    function(script, ..., python = NULL) {
        script <- rlang::arg_match0(script, KrakenToolsScripts)
        KrakenTools$new(cmd = python, ..., script = script)
    }
)

KrakenTools <- R6Class(
    "KrakenTools",
    inherit = Python,
    private = list(
        combine_params = function(script) {
            script <- pkg_extdata("KrakenTools", paste0(script, ".py"))
            file_executable(script)
            c(script, super$combine_params())
        }
    )
)

KrakenToolsScripts <- c(
    "combine_kreports", "combine_mpa", "extract_kraken_reads",
    "filter_bracken_out", "fix_unmapped", "kreport2krona",
    "kreport2mpa", "make_kreport", "make_ktaxonomy"
)