ANNOVAR

R/cmd-ANNOVAR.R

@@ -0,0 +1,53 @@
+#' Run ANNOVAR
+#'
+#' The `ANNOVAR` is a tool designed to provide ultrafast all-in-one preprocessing
+#' and quality control for FastQ data.
+#' @param fq1,fq2 A string of fastq file path.
+#' @param ... `r rd_dots("ANNOVAR")`.
+#' @param ofile1,ofile2 A string of path to the output fastq file.
+#' @param ANNOVAR `r rd_cmd("ANNOVAR")`.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://github.com/WGLab/doc-ANNOVAR>
+#'
+#' `r rd_seealso()`
+#' @export
+ANNOVAR <- make_command(
+  "ANNOVAR",
+  function(
+    fq1,
+    ofile1,
+    ...,
+    fq2 = NULL,
+    ofile2 = NULL,
+    ANNOVAR = NULL
+  ){
+    assert_string(ANNOVAR, allow_empty = FALSE, allow_null = TRUE)
+    ANNOVAR$new(
+      cmd = ANNOVAR,
+      ...,
+      fq1 = fq1,
+      fq2 = fq2,
+      ofile1 = ofile1,
+      ofile2 = ofile2
+    )
+  }
+)
+
+ANNOVAR <- R6Class(
+  "ANNOVAR",
+  inherit = Command,
+  private = list(
+    alias = function() "ANNOVAR",
+    setup_help_params = function() "--help",
+    setup_command_params = function(fq1, fq2, ofile1, ofile2){
+      c(
+        arg0("-i", fq1),
+        if (!is.null(fq2)) arg0("-I", fq2) else NULL,
+        arg0("-o", ofile1),
+        if (!is.null(ofile2)) arg0("-O", ofile2) else NULL
+      )
+    }
+  )
+)