comparison ribowaltz.R @ 1:e25d81465c23 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1

0:8e903cb3f919

  "gtffile", "g", 1, "character",
  "codon_coverage_info", "Y", 1, "character",
  "cds_coverage_info", "Z", 1, "character",
  "psite_info_rdata", "O", 0, "character",
  "refseq_sep", "s", 0, "character",
  "params_duplicate_filterting", "d", 0, "character",
  "params_peridiocity_filterting", "l", 0, "character",
  "params_custom_filterting", "c", 0, "character",
  "params_psite_additional", "p", 0, "character",
  "params_coverage_additional", "C", 0, "character"

sep <- opt$refseq_sep
if (opt$refseq_sep == "") {
  sep <- NULL
}
# convert alignments in BAM files into list of data tables
reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep)

library("jsonlite")
# remove duplicate reads
if (!is.null(opt$params_duplicate_filterting)) {
  json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting)

  )
}

# selection of read lengths - periodicity filtering
if (!is.null(opt$params_peridiocity_filterting)) {
    json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
    reads_list <- length_filter(
      data = reads_list,
      length_filter_mode = "periodicity",
      periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
    )
}
# selection of read lengths - length range filtering
if (!is.null(opt$params_custom_filterting)) {
    json_custom_filterting <- fromJSON(opt$params_custom_filterting)
    reads_list <- length_filter(
      data = reads_list,
      length_filter_mode = "custom",
      length_range = json_custom_filterting$length_range
    )
}

# compute P-site offset
json_psite_additional <- fromJSON(opt$params_psite_additional)
psite_offset <- psite(

1:e25d81465c23

  "gtffile", "g", 1, "character",
  "codon_coverage_info", "Y", 1, "character",
  "cds_coverage_info", "Z", 1, "character",
  "psite_info_rdata", "O", 0, "character",
  "refseq_sep", "s", 0, "character",
  "indel_threshold", "t", 0, "integer",
  "params_duplicate_filterting", "d", 0, "character",
  "params_peridiocity_filterting", "l", 0, "character",
  "params_custom_filterting", "c", 0, "character",
  "params_psite_additional", "p", 0, "character",
  "params_coverage_additional", "C", 0, "character"

sep <- opt$refseq_sep
if (opt$refseq_sep == "") {
  sep <- NULL
}
# convert alignments in BAM files into list of data tables
reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep, indel_threshold = opt$indel_threshold)

library("jsonlite")
# remove duplicate reads
if (!is.null(opt$params_duplicate_filterting)) {
  json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting)

  )
}

# selection of read lengths - periodicity filtering
if (!is.null(opt$params_peridiocity_filterting)) {
  json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
  reads_list <- length_filter(
    data = reads_list,
    length_filter_mode = "periodicity",
    periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
  )
}
# selection of read lengths - length range filtering
if (!is.null(opt$params_custom_filterting)) {
  json_custom_filterting <- fromJSON(opt$params_custom_filterting)
  reads_list <- length_filter(
    data = reads_list,
    length_filter_mode = "custom",
    length_range = json_custom_filterting$length_range
  )
}

# compute P-site offset
json_psite_additional <- fromJSON(opt$params_psite_additional)
psite_offset <- psite(