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annotate helper.R @ 8:7c9170b7d9f6 draft

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planemo upload commit 5b03cf1a31307c262701d4f267972bd01be24311
author mingchen0919
date Thu, 26 Apr 2018 13:38:15 -0400
parents 2c663ddb8488
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1 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
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2 #'
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3 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
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4 #' The first column are short flags, the second column are argument masks, the third column
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5 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
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6 #' @param gtg_name the name of a running GTG.
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7 getopt_specification_matrix = function(specification_file,
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8 gtg_name = 'gtg',
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9 tool_dir = Sys.getenv('TOOL_DIR')) {
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10 df = read.csv(
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11 paste0(tool_dir, '/', specification_file),
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12 header = TRUE,
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13 stringsAsFactors = FALSE
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14 )
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15 # check if there are duplicated short flags
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16 short_flags = df[, 1]
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17 if (length(unique(short_flags)) < length(short_flags)) {
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18 cat('----Duplicated short flags found ----\n')
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19 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
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20 stop('Duplicated short flags are not allowed.')
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21 }
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22
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23 # use short flags to generate long flags
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24 long_flags = paste0('X_', df[, 1])
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25
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26 # specification matrix
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27 df2 = data.frame(
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28 long_flags = long_flags,
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29 short_flags = df[, 1],
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30 argument_mask = df[, 2],
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31 data_type = df[, 3]
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32 )
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33
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34 as.matrix(df2)
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35 }
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39 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
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40 #'
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41 #' @param dir the path to the directory for generating the file tree.
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42 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
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43 # define a recursive function to build html string of the file tree
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44 file_tree = function(dir = '.') {
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45 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
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46 report_files_path = Sys.getenv('REPORT_FILES_PATH')
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47 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
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48
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49 files = list.files(path = dir,
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50 recursive = FALSE,
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51 full.names = TRUE)
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52 # files also include directorys, need to remove directorys
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53 files = files[!dir.exists(files)]
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54 dirs = list.dirs(path = dir,
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55 recursive = FALSE,
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56 full.names = TRUE)
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57 tags$ul({
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58 if (length(files) > 0) {
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59 lapply(files, function(x) {
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60 path_end = tail(strsplit(x, '/')[[1]], 1)
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61 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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62 li_item = tags$li(tags$a(path_end, href = href_path))
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63 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
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64 li_item
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65 })
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66 }
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67 },
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68 {
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69 if (length(dirs) > 0) {
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70 lapply(dirs, function(x) {
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71 path_end = tail(strsplit(x, '/')[[1]], 1)
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72 # hide vakata-jstree-3.3.5 folder
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73 if (path_end != 'vakata-jstree-3.3.5') {
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74 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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75 li_item = tags$li(path_end, file_tree(x))
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76 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
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77 li_item
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78 }
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79 })
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80 }
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81 })
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82 }