Add files via upload

JASON_UROPA_queries_V9.R

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+
+
+
+#================================
+#
+# Initialization
+#
+#================================
+
+# Loading in libraries
+library(shiny)
+library(shinydashboard)
+#library(shinyBS)
+
+# Defining the parameters
+startpoint <- 1
+
+# User-defined functions
+
+JU_resformat <- function (var1, var2, var3, var4, var5, var6, var7, var8, distance_up, distance_down) {
+  var3_read <- gsub("[[:space:]]", "", unlist(strsplit(var3, ";")))
+  if (length (var3_read) <= 1) {
+    concatline <- paste("{","\"feature\"",":\"", var1,"\", ",
+                        "\"feature.anchor\"",":\"", var2,"\", ",
+                        "\"show.attribute\":\"", var3,"\", ",
+                        "\"internals\"",":\"", var4,"\", ",
+                        "\"attribute.value\"",":\"", var5,"\", ",
+                        "\"strand\"",":\"",var6,"\", ",
+                        "\"attribute.value\"",":\"", var7,"\", ",
+                        "\"direction\"",":\"", var8,"\", ",
+                        "\"distance\"",":","[",distance_up,", ",distance_down,"]","}", sep = ""
+    )
+  } else {
+    var3_conc <- paste ("[\"", var3_read[1], "\"", sep = "")
+    for (i in 2:length(var3_read)) {
+      var3_i <- var3_read[i]
+      var3_conc <- paste (var3_conc, paste (", \"", var3_i, "\"", sep = ""))
+    }
+    var3_conc <- paste (var3_conc, "]", sep = "")
+    concatline <- paste("{","\"feature\"",":\"", var1,"\", ",
+                        "\"feature.anchor\"",":\"", var2,"\", ",
+                        "\"show.attribute\":", var3_conc,", ",
+                        "\"internals\"",":\"", var4,"\", ",
+                        "\"filter.attribute\"",":\"", var5,"\", ",
+                        "\"attribute.value\"",":\"", var6,"\", ",
+                        "\"strand\"",":\"",var7,"\", ",
+                        "\"direction\"",":\"", var8,"\", ",
+                        "\"distance\"",":","[",distance_up,", ",distance_down,"]","}", sep = ""
+    )
+  }
+
+
+  return (concatline)
+}
+
+# Creating modules
+
+# First module
+#--------------------------------
+
+# A module to read the inputs
+# UI-part
+PrintTablesUI <-  function(id, label = "ui1UI") {
+
+  ns <- NS(id)
+  shinyUI(fluidRow(
+      box(background = "light-blue",title= "query...",width=2),
+
+        box(background = "light-blue",title= "JASON_UROPA_queries",
+
+        column(width = 6,
+               textInput(ns("var1"),"feature"),
+               textInput(ns("var6"),"attribute.value"),
+               textInput(ns("var5"),"filter.attribute"),
+               textInput(ns("var3"),"show.attribute"),
+              # bsTooltip("var3", "type attributes between quotation marks separated with comma",
+                        # "right", options = list(container = "body")),
+               sliderInput(ns("distance_up"), "distance_uptream", min = -10000, max = 10000, value = c(500)))
+                        ,
+
+        column(width = 6,
+               selectInput(ns("var7"),"strand",choices=c("+","-","both")),
+               selectInput(ns("var2"),"feature.anchor",choices=c("start","center","end")),
+               selectInput(ns("var4"),"internals",choices=c("none","center","any")),
+               selectInput(ns("var8"),"direction",choices=c("any_direction","upstream","downstream")),
+               sliderInput(ns("distance_down"), "distance_upstream",min = -10000, max = 10000, value = c(500)
+           )    )
+
+        )
+       )
+  )
+}
+
+# Server-part
+PrintTables <- function(input, output, session) {
+
+  strinputvars <- list(
+    var1_ret <- reactive({input$var1}),
+    var2_ret <- reactive({input$var2}),
+    var2_ret <- reactive({input$var3}),
+    var2_ret <- reactive({input$var4}),
+    var2_ret <- reactive({input$var5}),
+    var2_ret <- reactive({input$var6}),
+    var2_ret <- reactive({input$var7}),
+    var2_ret <- reactive({input$var8}),
+    distanceUp_ret <- reactive({input$distance_up}),
+    distanceDown_ret <- reactive({input$distance_down})
+  )
+  return(strinputvars)
+}
+
+
+#================================
+#
+# Program code
+#
+#================================
+
+# We'll save it in a variable `ui` so that we can preview it in the console
+ui <- dashboardPage(
+
+  dashboardHeader(title=div(img(src="site.logo.jpg"),"JASON_UROPA_queries")),
+  dashboardSidebar(
+    fluidRow(
+
+      column(width=12, 
+             selectInput("species_GTF","select species",choices=c("mus musculus","homo sapiens")),
+             radioButtons("gtf_files" ,"Select gtf file",
+                          c("gencode.v22.genes.gtf"="human","gencode.vM5.genes.gtf"="mouse","other"="other")),
+             uiOutput("textORdate"),
+
+              #fileInput("gtf files","Upload gtf file (tab-separated)"),
+             fileInput("file1", "Upload bed File")),
+
+      column(width=12,
+
+             selectInput("priority"," prioritized query",choices=c("FALSE","TRUE"))),
+
+
+      column(width = 12,
+             numericInput("NrQuery","Enter number of queries", 2, min=1, max=NaN),
+             actionButton("addqueries", "Add Module"),
+             actionButton("printres", "Print"))
+
+      )), dashboardBody(
+
+
+      div(id = "ui_zero"),
+      div(id = "ui_zero2")
+         )
+
+)
+
+
+
+server <- (function(input, output, session) {
+
+  output$textORdate <- renderUI({
+    #validate(
+    #   need(!is.null(input$gtffiles), "please select a input type")
+    # )
+    if(input$gtf_files =="other"){
+      fileInput("file2","Upload gtf file (tab-separated)")
+    }else{
+
+    }
+  })
+
+
+
+  # Print the tables (first module)
+  observeEvent(input$addqueries, {
+
+    for (counter in startpoint:input$NrQuery) {
+      ID <- paste0("c", counter)
+      insertUI("#ui_zero", "beforeEnd", PrintTablesUI(ID))
+      module_iterres <- callModule(PrintTables, ID)
+      assign (paste("var_", ID, sep = ""), value = module_iterres, pos = 1)
+      observeEvent(input$printres, {
+        outputID <- "example"
+        insertUI("#ui_zero2", "beforeEnd", uiOutput(outputID))
+        uiOutput(outputID)
+        resline <- paste("\"", "queries", "\"", ":[", sep = "")
+        output$example <- renderUI({
+          for (counter in startpoint:input$NrQuery) {
+            ID <- paste0("c", counter)
+            fieldname <- eval(parse(text = paste("var_", ID, sep = "")))
+            if (counter == startpoint) {
+              resline <- paste (resline, JU_resformat(fieldname[[1]](), fieldname[[2]](), fieldname[[3]](), fieldname[[4]](), fieldname[[5]](), fieldname[[6]](), fieldname[[7]](), fieldname[[8]](), fieldname[[9]](), fieldname[[10]]()), sep = "")
+            } else {
+              resline <- paste (resline, ",\n", JU_resformat(fieldname[[1]](), fieldname[[2]](), fieldname[[3]](), fieldname[[4]](), fieldname[[5]](), fieldname[[6]](), fieldname[[7]](), fieldname[[8]](), fieldname[[9]](), fieldname[[10]]()), sep = "")
+            }
+          }
+          resline <- paste (resline, "]",
+                            ",\n\"priority\": \"", input$priority, "\",\n",
+                            "\"gtf\": \"", input$file2$name, "\",\n",
+                            "\"bed\": \"", input$file1$name, "\"", sep = "")
+
+
+          write.table (resline, "configuration_file.txt", quote = F, col.names = F, row.names = F)
+        })
+      })
+    }
+  })
+})
+
+
+# Running the program
+shinyApp(ui = ui, server = server)
+