# install.packages("devtools")
devtools::install_github("selkamand/utilitybeltcli")

# Step 1: Load library
library(utilitybeltcli)

# Step 2: Define basic components of the tool (and the R function we want to produce that wraps it)
MosdepthWrapper <- CommandlineWrapper$new(
  base_command = "mosdepth",
  tool_title = "Mosdepth",
  tool_description = "simple R wrapper",
  function_name = "run_mosdepth"
)

# Step 3: describe the paramaters of the tool including:
#   (a) flags (–-verbose)
#   (b) arguments (-–threads <num_threads>)
#   (c) positional arguments (base_command <positional_arg>)
MosdepthWrapper$add_arg(name = "threads", prefix = "--threads")
MosdepthWrapper$add_flag(name = "d4", prefix = "--d4", default = FALSE)
MosdepthWrapper$add_pos(name = "prefix", required = TRUE)
MosdepthWrapper$add_pos(name = "bam_or_cram", required = TRUE)

# Step 4: produce the R function wrapper for the tool
MosdepthWrapper$create_function_wrapping_commandline_tool()