Mercurial > repos > mingchen0919 > aurora_htseq
view helper.R @ 9:578a96df8690 draft
planemo upload commit 1cb2dd80dcb431563edbe1e763b3dde3a1adb2ae-dirty
author | mingchen0919 |
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date | Wed, 25 Apr 2018 14:22:32 -0400 |
parents | 7c54fd452b8e |
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#' \code{getopt_specification_matrix} returns a getopt specification matrix. #' #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data. #' The first column are short flags, the second column are argument masks, the third column #' is data types. The fourth column are variable names used in the tool XML. These three columns are required. #' @param gtg_name the name of a running GTG. getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) { df = read.csv( paste0(tool_dir, '/', specification_file), header = TRUE, stringsAsFactors = FALSE ) # check if there are duplicated short flags short_flags = df[, 1] if (length(unique(short_flags)) < length(short_flags)) { cat('----Duplicated short flags found ----\n') cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n') stop('Duplicated short flags are not allowed.') } # use short flags to generate long flags long_flags = paste0('X_', df[, 1]) # specification matrix df2 = data.frame( long_flags = long_flags, short_flags = df[, 1], argument_mask = df[, 2], data_type = df[, 3] ) as.matrix(df2) } #' \code{file_tree} generate file tree of a directory in the format of HTML lists. #' #' @param dir the path to the directory for generating the file tree. #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files. # define a recursive function to build html string of the file tree file_tree = function(dir = '.') { # get the OUTPUT_DIR folder data: dataset_NUMBER_files report_files_path = Sys.getenv('REPORT_FILES_PATH') output_dir = tail(strsplit(report_files_path, '/')[[1]], 1) files = list.files(path = dir, recursive = FALSE, full.names = TRUE) # files also include directorys, need to remove directorys files = files[!dir.exists(files)] dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE) tags$ul({ if (length(files) > 0) { lapply(files, function(x) { path_end = tail(strsplit(x, '/')[[1]], 1) href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] li_item = tags$li(tags$a(path_end, href = href_path)) li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}') li_item }) } }, { if (length(dirs) > 0) { lapply(dirs, function(x) { path_end = tail(strsplit(x, '/')[[1]], 1) # hide vakata-jstree-3.3.5 folder if (path_end != 'vakata-jstree-3.3.5') { # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2] li_item = tags$li(path_end, file_tree(x)) li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}') li_item } }) } }) }