Mercurial > repos > ethevenot > univariate

annotate univariate_wrapper.R @ 5:5687435b182c draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 957d0e442c875f7cf8461866fac9695175ab371b
author ethevenot
date Wed, 28 Feb 2018 06:29:34 -0500
parents 3017385625f6
children
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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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3 library(batch) ## parseCommandArgs
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4
4
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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5 # Constants
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6 argv <- commandArgs(trailingOnly = FALSE)
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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8 prog.name <- basename(script.path)
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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9
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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10 # Print help
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11 if (length(grep('-h', argv)) >0) {
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12 cat("Usage:", prog.name,
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13 "dataMatrix_in myDataMatrix.tsv",
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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14 "sampleMetadata_in mySampleData.tsv",
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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15 "variableMetadata_in myVariableMetadata.tsv",
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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16 "facC qual",
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17 "tesC kruskal",
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18 "adjC fdr",
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19 "thrN 0.05",
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20 "variableMetadata_out myVariableMetadata_out.tsv",
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21 "figure figure.pdf",
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22 "information information.txt",
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23 "\n")
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24 quit(status = 0)
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25 }
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26
0
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27 source_local <- function(fname){
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28 argv <- commandArgs(trailingOnly = FALSE)
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29 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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30 source(paste(base_dir, fname, sep="/"))
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31 }
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33 source_local("univariate_script.R")
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35 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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37 ##------------------------------
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38 ## Initializing
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39 ##------------------------------
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41 ## options
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42 ##--------
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44 strAsFacL <- options()$stringsAsFactors
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45 options(stringsAsFactors = FALSE)
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47 ## packages
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48 ##---------
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50 library(PMCMR)
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52 ## constants
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53 ##----------
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54
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55 modNamC <- "Univariate" ## module name
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56
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57 topEnvC <- environment()
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58 flagC <- "\n"
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60 ## functions
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61 ##----------
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62
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63 flgF <- function(tesC,
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64 envC = topEnvC,
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65 txtC = NA) { ## management of warning and error messages
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66
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67 tesL <- eval(parse(text = tesC), envir = envC)
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69 if(!tesL) {
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71 sink(NULL)
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72 stpTxtC <- ifelse(is.na(txtC),
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73 paste0(tesC, " is FALSE"),
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74 txtC)
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75
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76 stop(stpTxtC,
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77 call. = FALSE)
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78
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79 }
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80
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81 } ## flgF
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82
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83 ## log file
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84 ##---------
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85
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86 sink(argVc["information"])
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87
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88 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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89 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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90
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91 ## loading
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92 ##--------
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93
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94 datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
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95 check.names = FALSE,
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96 header = TRUE,
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97 row.names = 1,
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98 sep = "\t")))
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99
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100 samDF <- read.table(argVc["sampleMetadata_in"],
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101 check.names = FALSE,
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102 header = TRUE,
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103 row.names = 1,
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104 sep = "\t")
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105
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106 varDF <- read.table(argVc["variableMetadata_in"],
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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107 check.names = FALSE,
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108 header = TRUE,
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109 row.names = 1,
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110 sep = "\t")
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111
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112 tesC <- argVc["tesC"]
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113
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114 ## checking
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115 ##---------
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116
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117 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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118 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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119
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120 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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121 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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122
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123 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"))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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124 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"))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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125 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"))
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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126
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127 flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
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128
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129 flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
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130 txtC = "(corrected) p-value threshold must be between 0 and 1")
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131
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132
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133 ##------------------------------
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134 ## Computation
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135 ##------------------------------
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136
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137
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parents:
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138 varDF <- univariateF(datMN = datMN,
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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139 samDF = samDF,
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140 varDF = varDF,
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141 facC = argVc["facC"],
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142 tesC = tesC,
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143 adjC = argVc["adjC"],
3
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parents: 2
diff changeset
144 thrN = as.numeric(argVc["thrN"]),
140290de7986 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
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145 pdfC = argVc["figure"])
0
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146
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147
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148 ##------------------------------
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149 ## Ending
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150 ##------------------------------
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151
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152
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153 ## saving
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154 ##--------
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155
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156 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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157 varDF)
2
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parents: 0
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158
0
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159 write.table(varDF,
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160 file = argVc["variableMetadata_out"],
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161 quote = FALSE,
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162 row.names = FALSE,
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163 sep = "\t")
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164
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165 ## closing
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
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166 ##--------
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167
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168 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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169 as.character(Sys.time()), "\n", sep = "")
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170
4
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parents: 3
diff changeset
171 cat("\n\n\n============================================================================")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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172 cat("\nAdditional information about the call:\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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173 cat("\n1) Parameters:\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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174 print(cbind(value = argVc))
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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175
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176 cat("\n2) Session Info:\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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177 sessioninfo <- sessionInfo()
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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178 cat(sessioninfo$R.version$version.string,"\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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diff changeset
179 cat("Main packages:\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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diff changeset
180 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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parents: 3
diff changeset
181 cat("Other loaded packages:\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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diff changeset
182 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3017385625f6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit a81d4cc1df719dcc66def660927abda74972afaa
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183
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diff changeset
184 cat("============================================================================\n")
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185
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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parents:
diff changeset
186 sink()
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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187
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188 options(stringsAsFactors = strAsFacL)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
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189
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190 rm(list = ls())