update shiny app

ui <- fluidPage(

  # Application title

  titlePanel("zUMIs-config: Generate yaml file"),

   navlistPanel(widths = c(2, 10),

  navlistPanel(id = "mainNav",widths = c(2, 10),

               tabPanel("Mandatory Parameters",

                        #set basic things

                        fluidRow(

                            textInput("downsamp",label = "Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000). 0 invokes adaptive downsampling.",value = "0"),

                            selectInput("strand",label = "Is the library stranded?",choices = c("unstranded" = 0, "positively stranded" = 1, "negatively stranded" = 2),selected = "unstranded",multiple = F),

                            numericInput("HamDist","Hamming distance collapsing of UMI sequences:",value=0,min=0,max=5,step=1),

       checkboxInput("doVelocity",label="Generate velocyto-compatible counting of intron-exon spanning reads",value = F),

                            checkboxInput("doVelocity",label="Generate velocyto-compatible counting of intron-exon spanning reads. ATTENTION! This option is currently not implemented!",value = F),

                            checkboxInput("countPrimary",label="Count the primary Hits of multimapping reads towards gene expression levels?",value = T),

                            checkboxInput("twoPass",label="Perform basic STAR twoPass mapping?",value = T)

                          )),

                        p(strong("Your YAML is nearly ready...")),

                        uiOutput("saveUI"),

                        actionButton(inputId = "SaveYAML",label = "Save YAML!")

# ),

# tabPanel("Load YAML",

#   p(strong("You can load an existing YAML for zUMIs here")),

#   textInput(inputId="inYAML", label="Full path to YAML file", placeholder="eg: /path/to.yaml"),

#   actionButton(inputId = "LoadYAML",label = "Load YAML!")

                         ),

                         tabPanel("Load YAML",

                           p(strong("You can load an existing YAML for zUMIs here")),

                           textInput(inputId="inYAML", label="Full path to YAML file", placeholder="eg: /path/to.yaml"),

                           actionButton(inputId = "LoadYAML",label = "Load YAML!"),

                           p(strong("Please click the Load button twice for all options to be properly set in shiny! Sorry for the inconvenience."))

               )

  ))

  }

  observeEvent(input$LoadYAML, {

    if(file.exists(input$inYAML)){

      ya <- read_yaml(file = input$inYAML)

      print(paste("Loading",input$inYAML))

      loading_func(input$inYAML)

      updateNavlistPanel(session = session, inputId = "mainNav",selected = "Mandatory Parameters")

      }else{

        print("File doesn't exist!")

      }

  })

  loading_func <- function(myYAML){

      ya <- read_yaml(file = myYAML)

      updateTextInput(session = session,inputId = "runID",value = ya$project)

      updateTextInput(session = session,inputId = "outDir",value = ya$out_dir)

      updateTextInput(session = session,inputId = "STARpath",value = ya$reference$STAR_index)

      if(length(ya$reference$additional_files)>0){

        for(i in 1:length(ya$reference$additional_files)){

          updateTextInput(session = session,inputId = paste0("FA_",i), value = ya$reference$additional_files[i])

          print(input[[paste0("FA_",i)]])

        }

      }

      updateSliderInput(session = session, inputId = "nfiles", value = length(ya$sequence_files))

      for(i in 1:length(ya$sequence_files)){

        updateTextInput(session = session,inputId = paste0("fqpath_",i), value = ya$sequence_files[[i]]$name)

        if(any(grepl("BC",ya$sequence_files[[i]]$base_definition))){

          bc_string <- grep("BC",ya$sequence_files[[i]]$base_definition,value = T)

          bc_string <- substr(bc_string,start = 4, stop = nchar(bc_string)-1)

          updateTextInput(session = session,inputId = paste0("BC_",i), value = bc_string)

        }

        if(any(grepl("UMI",ya$sequence_files[[i]]$base_definition))){

          umi_string <- grep("UMI",ya$sequence_files[[i]]$base_definition,value = T)

          umi_string <- substr(umi_string,start = 5, stop = nchar(umi_string)-1)

          updateTextInput(session = session,inputId = paste0("UMI_",i), value = umi_string)

        }

        if(any(grepl("cDNA",ya$sequence_files[[i]]$base_definition))){

          cdna_string <- grep("cDNA",ya$sequence_files[[i]]$base_definition,value = T)

          cdna_string <- substr(cdna_string,start = 6, stop = nchar(cdna_string)-1)

          updateTextInput(session = session,inputId = paste0("cDNA_",i), value = cdna_string)

        }

      }

      updateNumericInput(session = session, inputId = "BCbases", value = ya$filter_cutoffs$BC_filter$num_bases)

      updateNumericInput(session = session, inputId = "BCphred", value = ya$filter_cutoffs$BC_filter$phred)

      updateNumericInput(session = session, inputId = "UMIbases", value = ya$filter_cutoffs$UMI_filter$num_bases)

      updateNumericInput(session = session, inputId = "UMIphred", value = ya$filter_cutoffs$UMI_filter$phred)

      updateNumericInput(session = session, inputId = "numThreads", value = ya$num_threads)

      updateNumericInput(session = session, inputId = "memLimit", value = ya$mem_limit)

      updateCheckboxInput(session = session, inputId = "makeStats", value = ya$make_stats)

      updateCheckboxInput(session = session, inputId = "useSLURM", value = ya$use_SLURM)

      updateSelectInput(session = session, inputId = "whichStage", selected = ya$which_Stage)

      updateCheckboxInput(session = session, inputId = "countIntrons", value = ya$counting_opts$introns)

      updateTextInput(session = session, inputId = "downsamp", value = ya$counting_opts$downsampling)

      updateSelectInput(session = session, inputId = "strand", selected = ya$counting_opts$strand)

      updateNumericInput(session = session, inputId = "HamDist", value = ya$counting_opts$Ham_Dist)

      updateCheckboxInput(session = session, inputId = "doVelocity", value = ya$counting_opts$velocyto)

      updateCheckboxInput(session = session, inputId = "countPrimary", value = ya$counting_opts$primaryHit)

      updateCheckboxInput(session = session, inputId = "twoPass", value = ya$counting_opts$twoPass)

      if (is.null(ya$barcodes$barcode_num & ya$barcodes$barcode_file)) {

        updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Automatic")

      }

      if (!is.null(ya$barcodes$barcode_file)){

        updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Barcod whitelist")

        updateTextInput(session = session, inputId = "BCfile", value = ya$barcodes$barcode_file)

      }

      if (!is.null(ya$barcodes$barcode_num)){

        updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Number of top Barcodes")

        updateNumericInput(session = session, inputId = "BCnum", value = ya$barcodes$barcode_num)

      }

      updateNumericInput(session = session, inputId = "HamBC", value = ya$barcodes$BarcodeBinning)

      updateNumericInput(session = session, inputId = "nReadsBC", value = ya$barcodes$nReadsperCell)

    }else{

      print("File doesn't exist!")

  }

  })

}