In MingChen0919/elagator: Assist in developing ELAstic GAlaxy TOols in R

knitr::opts_chunk$set(error = TRUE)

User input

knitr::kable(arguments)

# each tool execution runs one or multiple chained functions but generate only one single object.
# we save this object to an rdata file and output this file to galaxy history so that it can be used by other tools
# we can use this rdata output file's dataset id as the variable name of the saved object.
job_script_path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/job-script.R')
tool_rdata_output = Sys.getenv('TOOL_RDATA_OUTPUT')
dataset_id = tail(strsplit(tool_rdata_output, '/')[[1]], 1)
dataset_num = gsub("(.+_)([0-9]+)\\.dat", "\\2", dataset_id)
rdata_id = paste0('rdata_', dataset_num)

## build script
# the first line of the job script is 'rdata_NUM = ', where 'NUM' is the dataset number of the output rdata.
write(paste0(rdata_id, ' = '), file = job_script_path)
# loop through argument data frame to build up the job script.
for (i in 1: (nrow(arguments)-1)) {
  row_type = arguments[i, 'row_type']
  switch (row_type,
    # if it's a function row, the line has format 'function_name('
    func = write(paste0(arguments[i, 'function_name'], '('), 
                 file = job_script_path, 
                 append = TRUE ),


    argument = {
      # if it's an argument row and the next row is not an operator row,
      # the line has format '    argument_name=argument_value,'
      if (arguments[i+1, 'operator'] == "") {
        write(paste0('    ', arguments[i, 'argument_name'], '=', arguments[i, 'argument_value'], ','),
              file = job_script_path,
              append = TRUE )
      } else {
        # if it's an argument row and the next row IS an operator row,
        # the line has format '    argument_name=argument_value'. note that there is not comma at the end.
        write(paste0('    ', arguments[i, 'argument_name'], '=', arguments[i, 'argument_value']),
              file = job_script_path,
              append = TRUE )
      }
    },

    # if it is an operator row, the line has format ')  operator'
    operator =  write(paste0(')  ', arguments[i, 'operator']), 
                      file = job_script_path, 
                      append = TRUE )
  )
}

# the last line is missing a ')'
write(')', file = job_script_path, append = TRUE)

{bash, 'display script', results='asis', echo=FALSE} echo '## Job script' echo '' echo '' echo 'r' cat ${REPORT_FILES_PATH}/job-script.R echo '```'

## Result

```r
source(job_script_path)
# display result.
eval(parse(text = rdata_id))

## after the job is done, we list all files from the output directory.
## full relative path to the output directory needs to be displayed.

cat('##All output files')
cat('\n\n')
all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'), 
                       full.names = TRUE, 
                       recursive = TRUE)

for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
  cat('* [', f, '](', f, ')\n')
}
cat('\n')

MingChen0919/elagator documentation built on May 17, 2019, 6:22 p.m.