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annotate charts.r @ 1:344ac3ca7557 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
author iuc
date Wed, 17 Nov 2021 09:06:59 +0000
parents a87a3773d8ed
children
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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1 #!/usr/bin/Rscript
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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3 # load getopt library
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4 library("getopt");
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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6 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
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7 split <- function(argument) {
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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8 # process parameter string
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9 options <- list()
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10 list <- gsub("\\s", "", argument)
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11 list <- strsplit(list, ",")
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12 if (length(list) > 0) {
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13 list <- list[[1]]
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14 for (entry in list) {
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15 pair <- strsplit(entry, ":")
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16 if (length(pair) > 0) {
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17 pair <- pair[[1]]
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18 if (length(pair) == 2) {
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19 options[[pair[1]]] <- pair[2]
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20 }
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21 }
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22 }
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23 }
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24 return(options)
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25 }
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a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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27 # get options, using the spec as defined by the enclosed list.
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28 spec <- matrix(c(
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29 "workdir", "w", 1, "character", "Work directory",
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30 "module", "m", 1, "character", "Module name",
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31 "input", "i", 1, "character", "Input tabular file",
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32 "columns", "c", 1, "character", "Columns string",
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33 "settings", "s", 1, "character", "Settings string",
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34 "output", "o", 1, "character", "Output tabular file",
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35 "help", "h", 0, "", "Help",
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36 "verbose", "v", 0, "", "Verbose"
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37 ), byrow = TRUE, ncol = 5);
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38 opt <- getopt(spec);
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39
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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40 # show help
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41 if (!is.null(opt$help) ||
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42 is.null(opt$module) ||
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43 is.null(opt$input) ||
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44 is.null(opt$columns) ||
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45 is.null(opt$output)) {
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46 cat(getopt(spec, usage = TRUE))
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47 q(status = 1);
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48 }
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49
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50 # read columns/settings
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51 columns <- split(opt$columns)
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52 settings <- split(opt$settings)
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53
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54 # read table
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55 table <- read.table(opt$input, comment.char = "#", fill = TRUE)
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57 # identify module file
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58 module_file <- paste(opt$workdir, opt$module, ".r", sep = "")
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60 # source module
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61 source(module_file)
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63 # run module
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64 l <- wrapper(table, columns, settings)
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66 # header
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67 header_title <- "# title - Chart Utilities (charts)"
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68 header_date <- paste("# date -", Sys.time(), sep = " ")
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69 header_module <- paste("# module -", opt$module, sep = " ")
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70 header_settings <- paste("# settings -", opt$settings, sep = " ")
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71 header_columns <- paste("# columns -", opt$columns, sep = " ")
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73 # check result
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74 if (length(l) > 0) {
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75 # print details
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76 if (!is.null(opt$verbose)) {
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77 print("Columns:")
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78 print(columns)
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79 print("Settings:")
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80 print(settings)
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81 print("Result:")
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82 print(l)
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83 }
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84
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85 # create output file
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86 output <- file(opt$output, open = "wt")
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87
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88 # write header
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89 writeLines("#", output)
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90 writeLines(header_title, output)
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91 writeLines(header_date, output)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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92 writeLines(header_module, output)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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93 writeLines(header_settings, output)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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94 writeLines(header_columns, output)
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95 writeLines("#", output)
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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96
0
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97 # pad columns
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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98 rows <- max(unlist(lapply(l, length)))
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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99 padded <- lapply(l, function(col) {
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100 length(col) <- rows;
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101 col
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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102 })
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344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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103
0
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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104 # write table
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105 write.table(padded, file = output, row.names = FALSE, col.names = FALSE, quote = FALSE, sep = "\t")
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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106
0
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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107 # close file
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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108 close(output)
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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109 } else {
a87a3773d8ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b
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110 # print details
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111 print("Columns:")
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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112 print(columns)
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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113 print("Settings:")
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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114 print(settings)
344ac3ca7557 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 4494db13b69987fbc97d47177d2a5956e46e927b"
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115 print("No output generated.")
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116 }