comparison ribowaltz_plot.R @ 1:e25d81465c23 draft default tip

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

0:8e903cb3f919

    plot_title = "sample.transcript.length_range"
  )
  print(metaprofile)
  sample_list <- list()
  for (sample_name in names(reads_psite_list)) {
  sample_list[[sample_name]] <- c(sample_name)
  }
  metaheatmap <- metaheatmap_psite(
    reads_psite_list,
    annotation_dt,
    sample = sample_list,

if (!is.null(opt$params_codon_usage_psite)) {
  pdf("codon_usage.pdf", height = 6, width = 16)
  json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
  for (sample_name in names(reads_psite_list)) {
  cu_barplot <- codon_usage_psite(
    reads_psite_list,
    annotation_dt,
    sample = sample_name,
    fastapath = json_codon_usage_psite$fastapath,
    fasta_genome = FALSE,
    frequency_normalization = json_codon_usage_psite$frequency
  )
  print(cu_barplot[["plot"]])
  }
  dev.off()
}

1:e25d81465c23

    plot_title = "sample.transcript.length_range"
  )
  print(metaprofile)
  sample_list <- list()
  for (sample_name in names(reads_psite_list)) {
    sample_list[[sample_name]] <- c(sample_name)
  }
  metaheatmap <- metaheatmap_psite(
    reads_psite_list,
    annotation_dt,
    sample = sample_list,

if (!is.null(opt$params_codon_usage_psite)) {
  pdf("codon_usage.pdf", height = 6, width = 16)
  json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
  for (sample_name in names(reads_psite_list)) {
    cu_barplot <- codon_usage_psite(
      reads_psite_list,
      annotation_dt,
      sample = sample_name,
      fastapath = json_codon_usage_psite$fastapath,
      fasta_genome = FALSE,
      frequency_normalization = json_codon_usage_psite$frequency
    )
    print(cu_barplot[["plot"]])
  }
  dev.off()
}