Merge pull request #21 from SunPast/varscan

add varscan

Author: Yunuuuu

NAMESPACE

@@ -40,6 +40,7 @@ export(trust4)
 export(trust4_gene_names)
 export(trust4_imgt_annot)
 export(uninstall_appmamba)
+export(varscan)
 importFrom(R6,R6Class)
 importFrom(rlang,":=")
 importFrom(rlang,.data)

R/cmd-varscan.R

@@ -0,0 +1,45 @@
+#' VarScan is a platform-independent software tool 
+#' developed at the Genome Institute at Washington University to detect variants in NGS data.
+#'
+#' @param subcmd Sub-Command of varscan. Details see: `r rd_help("varscan")`.
+#' @param ... `r rd_dots("varscan")`.
+#' @param varscan `r rd_cmd("varscan")`.
+#' @seealso
+#' - <https://varscan.sourceforge.net/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+varscan <- make_command(
+  "varscan",
+  function(
+    subcmd = NULL,
+    ...,
+    varscan = NULL
+    ) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(varscan, allow_empty = FALSE, allow_null = TRUE)
+    Varscan$new(
+      cmd = varscan,
+      ...,
+      subcmd = subcmd
+    )
+  }
+)
+
+Varscan <- R6Class(
+  "Varscan",
+  inherit = Command,
+  private = list(
+    alias = function() "varscan",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd) {
+      if (private$help) {
+        c(super$combine_params(), subcmd)
+      } else {
+        c(subcmd, super$combine_params())
+      }
+    }
+  )
+)