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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 } |
