diff user_input_functions.R @ 0:56d5be6c03b9 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/user_input_functions.R	Fri Mar 08 06:30:11 2019 -0500
@@ -0,0 +1,197 @@
+# defining functions for checking user inputs
+
+# requesting directory input----------------------------------------------------------
+dir_input <- function(prompt) {
+  check <- FALSE
+  while(check == FALSE) {
+    user_input <- readline(prompt)
+    check <- dir.exists(user_input)
+    if(check==FALSE) {
+      msg <- sprintf("The directory: %s not found.", user_input)
+      message(msg)
+    }
+  }
+  return(user_input)
+}
+
+# requesting file input
+file_input <- function(prompt, directory) {
+  check <- FALSE
+  while(check == FALSE) {
+    user_input <- readline(prompt)
+    check <- file.exists(file.path(directory, user_input))
+    if(check==FALSE) {
+      msg <- sprintf("File: %s not found.", user_input)
+      message(msg)
+    }
+  }
+  return(user_input)
+}
+
+# requesting string input------------------------------------------------------------
+string_input <- function(prompt) {
+  check <- FALSE
+  while(check == FALSE) {
+    user_input <- readline(prompt)
+    check <- user_input!=''
+    if(check == FALSE) {
+      message("Input can't be empty.")
+    }
+  }
+  return(user_input)
+}
+
+# requesting integer input----------------------------------------------------------
+numeric_input <- function(prompt, default) {
+  check <- FALSE
+  while(check == FALSE) {
+    user_input <- readline(prompt)
+    
+    # if blank, set user_input to defalut
+    if(user_input == '') {
+      user_input <- default
+      msg <- sprintf("No input supplied, default of %s used.", default)
+      message(msg)
+    }
+    # coerce input to be numeric
+    else {
+      user_input <- as.numeric(user_input) 
+    }
+    # check if number supplied
+    check <- !is.na(user_input)
+    if(check == FALSE) {
+      message("Input must be a number.")
+    }
+  }
+  return(user_input)
+}
+
+# request constrained string---------------------------------------------------------
+# default is numeric, referring to the index of desired option in 'choices'
+cons_string_input <- function(prompt, choices, default) {
+  
+  if(missing(default)){
+    check <- FALSE
+    while(check == FALSE) {
+      user_input <- as.numeric(menu(choices, graphics=FALSE, title=prompt))
+      user_input <- choices[user_input]
+      
+      check <- user_input!=''
+      if(check == FALSE) message("Input can't be empty.")
+      else message(sprintf("\nSelected: %s", user_input))
+    }
+  }
+  
+  if(!missing(default)){
+    # setting up prompt with menu
+    num_choices <- str_c(1:length(choices), choices, sep='. ')
+    menu_prompt <- sprintf("%s\n\t%s\n", prompt, str_c(num_choices, collapse='\n\t'))
+    message(menu_prompt)
+    
+    # requesting user input
+    user_input <- readline("Selection:")
+    
+    # setting default
+    if(user_input == '') {
+      user_input <- as.numeric(default)
+      user_input <- choices[user_input]
+      msg <- sprintf("No input supplied, default of %s used.", user_input)
+      message(msg)
+    }
+    else {
+      user_input <- as.numeric(user_input)
+      user_input <- choices[user_input]
+      message(sprintf("\nSelected: %s", user_input))
+    }
+  }
+  
+  return(user_input)
+}
+
+# request multiple inputs-----------------------------------------------------------
+## default is optional; can set default to NULL if want to allow blank entry
+cons_string_mult <- function(prompt, choices, default) {
+  if(missing(default)) {
+    check <- FALSE
+    while(check == FALSE) {
+      user_input <- select.list(choices=choices, multiple=TRUE, title=prompt, 
+                                graphics = FALSE)
+      
+      if(length(user_input)==0)  {
+        message("Input can't be empty.")
+        check <- FALSE
+      }
+      else {
+        message(sprintf("\nSelected: %s", user_input))
+        check <- TRUE
+      }
+    }
+  }
+  
+  if(!missing(default)) {
+    user_input <- select.list(choices=choices, multiple=TRUE, title=prompt, 
+                              graphics=FALSE)
+    
+    if(length(user_input)==0) {
+      if(is.null(default)) user_input <- default
+      else user_input <- default
+      msg <- sprintf("No input supplied, using default:%s", 
+                     paste(user_input, collapse=', '))
+      message(msg)
+    }
+    
+  }
+  
+  return(user_input)
+  
+}
+
+# yesno input-------------------------------------------------------------------
+# default is TRUE or FALSE
+yn_input <- function(prompt, default) {
+  
+  choices <- c("Yes", "No")
+  
+  if(missing(default)) {
+    check <- FALSE
+    while(check == FALSE) {
+      user_input <- menu(choices, graphics=FALSE, title=prompt)
+      
+      if(length(user_input)==0)  {
+        message("Input can't be empty.")
+        check <- FALSE
+      }
+      else {
+        message(sprintf("\nSelected: %s", user_input))
+        check <- TRUE
+      }
+    }
+    user_input <- ifelse(user_input == 1L, TRUE, FALSE)
+  }
+  if(!missing(default)) {
+    
+    # setting up prompt with menu
+    num_choices <- str_c(1:length(choices), choices, sep='. ')
+    menu_prompt <- sprintf("%s\n\t%s\n", prompt, str_c(num_choices, collapse='\n\t'))
+    message(menu_prompt)
+    
+    # requesting user input
+    user_input <- readline("Selection:")
+    
+    # setting default
+    if(user_input == '') {
+      user_input <- as.numeric(default)
+      msg <- sprintf("No input supplied, default of %s used.", choices[user_input])
+      message(msg)
+      user_input <- ifelse(user_input == 1L, TRUE, FALSE)
+    }
+    else {
+      user_input <- as.numeric(user_input)
+      message(sprintf("\nSelected: %s", choices[user_input]))
+      user_input <- ifelse(user_input == 1L, TRUE, FALSE)
+    }
+  }
+  
+  
+  return(user_input)
+}
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