Mercurial > repos > ethevenot > univariate

annotate univariate_wrapper.R @ 2:09799fc16bc6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents ef64d3752050
children 140290de7986
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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1 #!/usr/bin/env Rscript
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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3 library(batch) ## parseCommandArgs
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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5 source_local <- function(fname){
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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6 argv <- commandArgs(trailingOnly = FALSE)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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8 source(paste(base_dir, fname, sep="/"))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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9 }
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11 source_local("univariate_script.R")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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13 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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15 ##------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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16 ## Initializing
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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17 ##------------------------------
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19 ## options
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20 ##--------
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22 strAsFacL <- options()$stringsAsFactors
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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23 options(stringsAsFactors = FALSE)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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25 ## packages
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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26 ##---------
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28 library(PMCMR)
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30 ## constants
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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31 ##----------
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33 modNamC <- "Univariate" ## module name
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35 topEnvC <- environment()
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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36 flagC <- "\n"
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38 ## functions
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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39 ##----------
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41 flgF <- function(tesC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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42 envC = topEnvC,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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43 txtC = NA) { ## management of warning and error messages
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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45 tesL <- eval(parse(text = tesC), envir = envC)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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47 if(!tesL) {
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49 sink(NULL)
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50 stpTxtC <- ifelse(is.na(txtC),
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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51 paste0(tesC, " is FALSE"),
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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52 txtC)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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54 stop(stpTxtC,
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55 call. = FALSE)
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57 }
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58
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59 } ## flgF
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60
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61 ## log file
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62 ##---------
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63
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64 sink(argVc["information"])
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65
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66 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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67 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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68
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69 ## loading
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70 ##--------
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71
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72 datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
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73 check.names = FALSE,
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74 header = TRUE,
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75 row.names = 1,
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76 sep = "\t")))
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77
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78 samDF <- read.table(argVc["sampleMetadata_in"],
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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79 check.names = FALSE,
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80 header = TRUE,
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81 row.names = 1,
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82 sep = "\t")
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83
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84 varDF <- read.table(argVc["variableMetadata_in"],
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85 check.names = FALSE,
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86 header = TRUE,
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87 row.names = 1,
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88 sep = "\t")
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89
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90 tesC <- argVc["tesC"]
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91
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92 ## checking
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93 ##---------
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94
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95 flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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96 flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
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97
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98 flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata"))
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99 flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only"))
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101 flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes"))
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102 flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes"))
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103 flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only"))
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104
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105 flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
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106
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107 flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
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108 txtC = "(corrected) p-value threshold must be between 0 and 1")
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109
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110
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111 ##------------------------------
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112 ## Computation
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113 ##------------------------------
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114
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115
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116 varDF <- univariateF(datMN = datMN,
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117 samDF = samDF,
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118 varDF = varDF,
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119 facC = argVc["facC"],
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120 tesC = tesC,
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121 adjC = argVc["adjC"],
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122 thrN = as.numeric(argVc["thrN"]))
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123
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124
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125 ##------------------------------
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126 ## Ending
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127 ##------------------------------
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128
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129
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130 ## saving
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131 ##--------
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132
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133 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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134 varDF)
2
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135
0
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136 write.table(varDF,
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137 file = argVc["variableMetadata_out"],
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138 quote = FALSE,
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139 row.names = FALSE,
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140 sep = "\t")
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141
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142 ## closing
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143 ##--------
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144
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145 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
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146 as.character(Sys.time()), "\n", sep = "")
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147
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148 sink()
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149
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150 options(stringsAsFactors = strAsFacL)
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151
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152 rm(list = ls())