comparison fastq_dump_pe_render.R @ 21:3c859d094074 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e

20:2167f32cf379

#           possible values: logical, integer, double, complex, character.
##------- 1. input data ---------------------
spec_list=list()
spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
spec_list$FORMAT = c('format', 'f', '1', 'character')
spec_list$ECHO = c('echo', 'e', '1', 'character')
##--------2. output report and outputs --------------
spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
##--------3. Rmd templates in the tool directory ----------

  }) %>%
  (function(x) {
    gsub('FORMAT', opt$format, x)
  }) %>%
  (function(x) {
    gsub('ECHO', opt$echo, x)
  }) %>%
  (function(x) {
    gsub('OUTPUT_DIR', opt$output_dir, x)
  }) %>%
  (function(x) {
    fileConn = file('fastq_dump_pe.Rmd')
    writeLines(x, con=fileConn)

21:3c859d094074

#           possible values: logical, integer, double, complex, character.
##------- 1. input data ---------------------
spec_list=list()
spec_list$SRA_ACCESSION = c('sra_accession', 'i', '1', 'character')
spec_list$FORMAT = c('format', 'f', '1', 'character')
##--------2. output report and outputs --------------
spec_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
spec_list$OUTPUT_DIR = c('output_dir', 'd', '1', 'character')
spec_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
##--------3. Rmd templates in the tool directory ----------

  }) %>%
  (function(x) {
    gsub('FORMAT', opt$format, x)
  }) %>%
  (function(x) {
    gsub('OUTPUT_DIR', opt$output_dir, x)
  }) %>%
  (function(x) {
    fileConn = file('fastq_dump_pe.Rmd')
    writeLines(x, con=fileConn)