ui.R

library(shinydashboard)
library(shinycustomloader)
shinyUI(dashboardPage(
  dashboardHeader(title = "Easy16S"),
  dashboardSidebar(
    tags$div(
      title = "Select dataset for demonstration",
      selectInput(
        "demo",
        label = "Select demo dataset : ",
        choices = list("Input data" = "input",
                       "Chaillou et al., 2015" = "food"),
        # "Mach et al., 2015" = "kinetic", "Morton et al., 2017" = "soil", "Ravel et al., 2011" = "ravel", "biorare" = "biorare", "GlobalPatterns" = "GlobalPatterns"
        selected = 1
      )
    ),
    hr(width = "90%"),
    tags$div(
      title = "Abundance BIOM file come from FROGS with 'FROGS BIOM to std BIOM', Qiime or another metagenomic tool.",
      fileInput("fileBiom",
                label = "Abundance BIOM file : ",
                placeholder = "data.biom"),
      radioButtons(
        "biomFormat",
        label = NULL,
        inline = TRUE,
        choices = list(`STD BIOM` = "std",
                       `FROGS BIOM` = "frogs"),
        selected = "std"
      )
    ),
    tags$div(
      style = "text-align:center",
      title = "Resample dataset such that all samples have the same library size. \nIt's using an random sampling without replacement.",
      checkboxInput("rareData", label = "Rarefy dataset", value = TRUE),
      textOutput("rarefactionMin")
    ),
    tags$div(
      title = "Metadata table with variables (in columns) and samples (in rows). \nMake sure you follow the exact spelling of the sample names (1st column). \nThe import of an excel table is possible but not recommended.",
      fileInput("fileMeta",
                label = "Metadata table : ",
                placeholder = "data.csv")
    ),
    radioButtons(
      "CSVsep",
      label = "CSV separator : ",
      inline = TRUE,
      choices = list(
        `<tab>` = "\t",
        `,` = ",",
        `;` = ";",
        excel = "excel"
      )
    ),
    tags$div(
      title = "Phylogenetic tree",
      fileInput("fileTree",
                label = "Phylogenetic tree : ",
                placeholder = "data.nwk")
    )#,
    # tags$div(
    #   title = "Representative FASTA sequences of OTU",
    #   fileInput(
    #     "fileSeq",
    #     label = "FASTA sequences : "),
    #     placeholder = "data.fasta"
    #   )
    # )
  ),
  dashboardBody(