Mercurial > repos > recetox > waveica

annotate waveica_wrapper.R @ 6:071a424241ec draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit bc3445f7c41271b0062c7674108f57708d08dd28
author recetox
date Thu, 30 May 2024 14:54:02 +0000
parents e424fa636281
children 1a2aeb8137bf
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6480c6d5fa36 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
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1 read_file <- function(file, metadata, ft_ext, mt_ext, transpose) {
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2 data <- read_data(file, ft_ext)
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4 if (transpose) {
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5 col_names <- c("sampleName", data[[1]])
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6 t_data <- data[-1]
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7 t_data <- t(t_data)
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8 data <- data.frame(rownames(t_data), t_data)
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9 colnames(data) <- col_names
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10 }
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12 if (!is.na(metadata)) {
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13 mt_data <- read_data(metadata, mt_ext)
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14 data <- merge(mt_data, data, by = "sampleName")
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15 }
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17 return(data)
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18 }
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20 read_data <- function(file, ext) {
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21 if (ext == "csv") {
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22 data <- read.csv(file, header = TRUE)
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23 } else if (ext == "tsv") {
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24 data <- read.csv(file, header = TRUE, sep = "\t")
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25 } else {
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26 data <- arrow::read_parquet(file)
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27 }
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29 return(data)
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30 }
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32 waveica <- function(file,
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33 metadata = NA,
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34 ext,
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35 transpose = FALSE,
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36 wavelet_filter,
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37 wavelet_length,
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38 k,
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39 t,
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40 t2,
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41 alpha,
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42 exclude_blanks) {
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43 # get input from the Galaxy, preprocess data
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44 ext <- strsplit(x = ext, split = "\\,")[[1]]
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46 ft_ext <- ext[1]
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47 mt_ext <- ext[2]
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49 data <- read_file(file, metadata, ft_ext, mt_ext, transpose)
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51 required_columns <- c(
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52 "sampleName", "class", "sampleType",
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53 "injectionOrder", "batch"
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54 )
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55 data <- verify_input_dataframe(data, required_columns)
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57 data <- sort_by_injection_order(data)
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59 # separate data into features, batch and group
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60 feature_columns <- colnames(data)[!colnames(data) %in% required_columns]
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61 features <- data[, feature_columns]
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62 group <- enumerate_groups(as.character(data$sampleType))
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63 batch <- data$batch
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65 # run WaveICA
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66 features <- recetox.waveica::waveica(
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67 data = features,
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68 wf = get_wf(wavelet_filter, wavelet_length),
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69 batch = batch,
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70 group = group,
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71 K = k,
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72 t = t,
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73 t2 = t2,
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74 alpha = alpha
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75 )
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77 data[, feature_columns] <- features
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79 # remove blanks from dataset
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80 if (exclude_blanks) {
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81 data <- exclude_group(data, group)
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82 }
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84 return(data)
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85 }
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87 waveica_singlebatch <- function(file,
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88 metadata = NA,
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89 ext,
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90 transpose = FALSE,
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91 wavelet_filter,
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92 wavelet_length,
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93 k,
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94 alpha,
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95 cutoff,
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96 exclude_blanks) {
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97 # get input from the Galaxy, preprocess data
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98 ext <- strsplit(x = ext, split = "\\,")[[1]]
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99
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100 ft_ext <- ext[1]
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101 mt_ext <- ext[2]
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102
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103 data <- read_file(file, metadata, ft_ext, mt_ext, transpose)
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104
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105 required_columns <- c("sampleName", "class", "sampleType", "injectionOrder")
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106 optional_columns <- c("batch")
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107
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108 data <- verify_input_dataframe(data, required_columns)
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109
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110 data <- sort_by_injection_order(data)
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111
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112 feature_columns <- colnames(data)[!colnames(data) %in% c(required_columns, optional_columns)]
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113 features <- data[, feature_columns]
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114 injection_order <- data$injectionOrder
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115
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116 # run WaveICA
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117 features <- recetox.waveica::waveica_nonbatchwise(
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118 data = features,
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119 wf = get_wf(wavelet_filter, wavelet_length),
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120 injection_order = injection_order,
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121 K = k,
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122 alpha = alpha,
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123 cutoff = cutoff
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124 )
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125
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126 data[, feature_columns] <- features
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127 group <- enumerate_groups(as.character(data$sampleType))
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128 # remove blanks from dataset
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129 if (exclude_blanks) {
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130 data <- exclude_group(data, group)
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131 }
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132
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133 return(data)
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134 }
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135
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136
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137 sort_by_injection_order <- function(data) {
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138 if ("batch" %in% colnames(data)) {
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139 data <- data[order(data[, "batch"], data[, "injectionOrder"], decreasing = FALSE), ]
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140 } else {
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141 data <- data[order(data[, "injectionOrder"], decreasing = FALSE), ]
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142 }
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143 return(data)
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144 }
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145
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146
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147 verify_input_dataframe <- function(data, required_columns) {
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148 if (anyNA(data)) {
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149 stop("Error: dataframe cannot contain NULL values!
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150 Make sure that your dataframe does not contain empty cells")
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151 } else if (!all(required_columns %in% colnames(data))) {
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152 stop(
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153 "Error: missing metadata!
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154 Make sure that the following columns are present in your dataframe: ",
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155 paste(required_columns, collapse = ", ")
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156 )
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157 }
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158
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159 data <- verify_column_types(data, required_columns)
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160
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161 return(data)
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162 }
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163
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164 verify_column_types <- function(data, required_columns) {
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165 # Specify the column names and their expected types
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166 column_types <- list(
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167 "sampleName" = c("character", "factor"),
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168 "class" = c("character", "factor", "integer"),
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169 "sampleType" = c("character", "factor"),
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170 "injectionOrder" = "integer",
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171 "batch" = "integer"
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172 )
2
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173
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174 column_types <- column_types[required_columns]
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175
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176 for (col_name in names(data)) {
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177 actual_type <- class(data[[col_name]])
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178 if (col_name %in% names(column_types)) {
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179 expected_types <- column_types[[col_name]]
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180
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181 if (!actual_type %in% expected_types) {
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182 stop(
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183 "Column ", col_name, " is of type ", actual_type,
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184 " but expected type is ",
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185 paste(expected_types, collapse = " or "), "\n"
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186 )
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187 }
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188 } else {
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189 if (actual_type != "numeric") {
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190 data[[col_name]] <- as.numeric(as.character(data[[col_name]]))
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191 }
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192 }
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193 }
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194 return(data)
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195 }
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197
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198 # Match group labels with [blank/sample/qc] and enumerate them
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199 enumerate_groups <- function(group) {
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200 group[grepl("blank", tolower(group))] <- 0
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201 group[grepl("sample", tolower(group))] <- 1
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202 group[grepl("qc", tolower(group))] <- 2
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203
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204 return(group)
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205 }
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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206
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207
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208 # Create appropriate input for R wavelets function
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209 get_wf <- function(wavelet_filter, wavelet_length) {
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210 wf <- paste(wavelet_filter, wavelet_length, sep = "")
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211
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212 # exception to the wavelet function
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213 if (wf == "d2") {
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214 wf <- "haar"
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215 }
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216
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217 return(wf)
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218 }
328710890963 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"
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220
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221 # Exclude blanks from a dataframe
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222 exclude_group <- function(data, group) {
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223 row_idx_to_exclude <- which(group %in% 0)
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224 if (length(row_idx_to_exclude) > 0) {
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225 data_without_blanks <- data[-c(row_idx_to_exclude), ]
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226 cat("Blank samples have been excluded from the dataframe.\n")
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227 return(data_without_blanks)
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228 } else {
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229 return(data)
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230 }
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231 }
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232
1
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233 store_data <- function(data, output, ext) {
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234 if (ext == "parquet") {
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235 arrow::write_parquet(data, output)
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236 } else {
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237 write.table(data,
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238 file = output, sep = "\t",
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239 row.names = FALSE, quote = FALSE
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240 )
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241 }
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242 cat("Normalization has been completed.\n")
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243 }