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6
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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, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
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8 df = read.csv(paste0(tool_dir, '/', specification_file),
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9 header = TRUE, stringsAsFactors = FALSE)
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10 # check if there are duplicated short flags
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11 short_flags = df[, 1]
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12 if (length(unique(short_flags)) < length(short_flags)) {
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13 cat('----Duplicated short flags found ----\n')
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14 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
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15 stop('Duplicated short flags are not allowed.')
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16 }
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17
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18 # use short flags to generate long flags
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19 long_flags = paste0('X_', df[, 1])
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20
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21 # specification matrix
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22 df2 = data.frame(long_flags = long_flags,
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23 short_flags = df[, 1],
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24 argument_mask = df[, 2],
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25 data_type = df[, 3])
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26
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27 as.matrix(df2)
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28 }
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29
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30
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31
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32 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
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33 #'
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34 #' @param dir the path to the directory for generating the file tree.
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35 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
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36 # define a recursive function to build html string of the file tree
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37 file_tree = function(dir = '.'){
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38 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
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39 report_files_path = Sys.getenv('REPORT_FILES_PATH')
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40 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
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41
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42 files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
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43 # files also include directorys, need to remove directorys
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44 files = files[!dir.exists(files)]
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45 dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
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46 # hide vakata-jstree-3.3.5 folder
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47 #jstree_index = grep(pattern = 'vakata-jstree-3.3.5', x = dirs)
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48 #dirs = dirs[-jstree_index]
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49 tags$ul(
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50 {
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51 if (length(files) > 0) {
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52 lapply(files, function(x){
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53 path_end = tail(strsplit(x, '/')[[1]],1)
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54 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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55 li_item = tags$li(tags$a(path_end, href=href_path))
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56 li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
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57 li_item
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58 })
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59 }
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60 },
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61 {
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62 if (length(dirs) > 0) {
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63 lapply(dirs, function(x){
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64 x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
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65 li_item = tags$li(x_path, file_tree(x))
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66 li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
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67 li_item
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68 })
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69 }
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70 }
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71 )
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72 }
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