Mercurial > repos > mingchen0919 > dynamic_tool_test
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planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
author | mingchen0919 |
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date | Wed, 21 Mar 2018 17:26:27 -0400 |
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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) }