Mercurial > repos > matthias > dada2_dada

annotate user_input_functions.R @ 8:441a137f4fbc draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 977f22125c9ad5c3c5560de8946017305c5633c1
author matthias
date Mon, 27 May 2019 13:27:16 -0400
parents 38959bdb0956
children
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38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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1 # defining functions for checking user inputs
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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2
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3 # requesting directory input----------------------------------------------------------
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4 dir_input <- function(prompt) {
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5 check <- FALSE
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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6 while(check == FALSE) {
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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7 user_input <- readline(prompt)
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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8 check <- dir.exists(user_input)
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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9 if(check==FALSE) {
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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10 msg <- sprintf("The directory: %s not found.", user_input)
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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11 message(msg)
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12 }
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13 }
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14 return(user_input)
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15 }
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16
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17 # requesting file input
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18 file_input <- function(prompt, directory) {
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19 check <- FALSE
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20 while(check == FALSE) {
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21 user_input <- readline(prompt)
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22 check <- file.exists(file.path(directory, user_input))
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23 if(check==FALSE) {
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24 msg <- sprintf("File: %s not found.", user_input)
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25 message(msg)
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26 }
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27 }
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28 return(user_input)
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29 }
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31 # requesting string input------------------------------------------------------------
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32 string_input <- function(prompt) {
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33 check <- FALSE
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34 while(check == FALSE) {
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35 user_input <- readline(prompt)
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36 check <- user_input!=''
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37 if(check == FALSE) {
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38 message("Input can't be empty.")
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39 }
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40 }
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41 return(user_input)
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42 }
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43
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44 # requesting integer input----------------------------------------------------------
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45 numeric_input <- function(prompt, default) {
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46 check <- FALSE
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47 while(check == FALSE) {
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48 user_input <- readline(prompt)
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49
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50 # if blank, set user_input to defalut
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51 if(user_input == '') {
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52 user_input <- default
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53 msg <- sprintf("No input supplied, default of %s used.", default)
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54 message(msg)
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55 }
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56 # coerce input to be numeric
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57 else {
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58 user_input <- as.numeric(user_input)
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59 }
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60 # check if number supplied
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61 check <- !is.na(user_input)
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62 if(check == FALSE) {
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63 message("Input must be a number.")
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64 }
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65 }
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66 return(user_input)
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67 }
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68
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69 # request constrained string---------------------------------------------------------
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70 # default is numeric, referring to the index of desired option in 'choices'
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71 cons_string_input <- function(prompt, choices, default) {
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72
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73 if(missing(default)){
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74 check <- FALSE
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75 while(check == FALSE) {
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76 user_input <- as.numeric(menu(choices, graphics=FALSE, title=prompt))
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77 user_input <- choices[user_input]
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78
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79 check <- user_input!=''
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80 if(check == FALSE) message("Input can't be empty.")
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81 else message(sprintf("\nSelected: %s", user_input))
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82 }
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83 }
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84
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85 if(!missing(default)){
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86 # setting up prompt with menu
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87 num_choices <- str_c(1:length(choices), choices, sep='. ')
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88 menu_prompt <- sprintf("%s\n\t%s\n", prompt, str_c(num_choices, collapse='\n\t'))
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89 message(menu_prompt)
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90
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91 # requesting user input
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92 user_input <- readline("Selection:")
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93
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94 # setting default
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95 if(user_input == '') {
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96 user_input <- as.numeric(default)
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97 user_input <- choices[user_input]
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98 msg <- sprintf("No input supplied, default of %s used.", user_input)
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99 message(msg)
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100 }
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101 else {
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102 user_input <- as.numeric(user_input)
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103 user_input <- choices[user_input]
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104 message(sprintf("\nSelected: %s", user_input))
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105 }
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106 }
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107
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108 return(user_input)
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109 }
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110
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111 # request multiple inputs-----------------------------------------------------------
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112 ## default is optional; can set default to NULL if want to allow blank entry
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113 cons_string_mult <- function(prompt, choices, default) {
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114 if(missing(default)) {
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115 check <- FALSE
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116 while(check == FALSE) {
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117 user_input <- select.list(choices=choices, multiple=TRUE, title=prompt,
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118 graphics = FALSE)
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119
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120 if(length(user_input)==0) {
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121 message("Input can't be empty.")
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122 check <- FALSE
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123 }
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124 else {
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125 message(sprintf("\nSelected: %s", user_input))
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126 check <- TRUE
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127 }
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128 }
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129 }
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130
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131 if(!missing(default)) {
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132 user_input <- select.list(choices=choices, multiple=TRUE, title=prompt,
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133 graphics=FALSE)
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134
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135 if(length(user_input)==0) {
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136 if(is.null(default)) user_input <- default
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137 else user_input <- default
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138 msg <- sprintf("No input supplied, using default:%s",
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139 paste(user_input, collapse=', '))
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140 message(msg)
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141 }
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142
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143 }
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144
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145 return(user_input)
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146
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147 }
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148
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149 # yesno input-------------------------------------------------------------------
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150 # default is TRUE or FALSE
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151 yn_input <- function(prompt, default) {
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152
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153 choices <- c("Yes", "No")
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154
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155 if(missing(default)) {
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156 check <- FALSE
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157 while(check == FALSE) {
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158 user_input <- menu(choices, graphics=FALSE, title=prompt)
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159
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160 if(length(user_input)==0) {
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161 message("Input can't be empty.")
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162 check <- FALSE
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163 }
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164 else {
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165 message(sprintf("\nSelected: %s", user_input))
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166 check <- TRUE
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167 }
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168 }
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169 user_input <- ifelse(user_input == 1L, TRUE, FALSE)
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170 }
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171 if(!missing(default)) {
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172
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173 # setting up prompt with menu
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174 num_choices <- str_c(1:length(choices), choices, sep='. ')
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175 menu_prompt <- sprintf("%s\n\t%s\n", prompt, str_c(num_choices, collapse='\n\t'))
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176 message(menu_prompt)
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177
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178 # requesting user input
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179 user_input <- readline("Selection:")
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180
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181 # setting default
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182 if(user_input == '') {
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183 user_input <- as.numeric(default)
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184 msg <- sprintf("No input supplied, default of %s used.", choices[user_input])
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185 message(msg)
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186 user_input <- ifelse(user_input == 1L, TRUE, FALSE)
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187 }
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188 else {
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189 user_input <- as.numeric(user_input)
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190 message(sprintf("\nSelected: %s", choices[user_input]))
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191 user_input <- ifelse(user_input == 1L, TRUE, FALSE)
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192 }
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193 }
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194
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195
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196 return(user_input)
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197 }