Commit a8cc0e6c authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

debug json load

parent d47b6843
......@@ -48,8 +48,8 @@ Project_box_result <- function(masque_key,curdir){
if(file.exists(annot_process))
{
ap = read.csv(annot_process,sep="\t")
if(json_data[[1]]$type == "16S") db_choices = c("Silva" = "silva","Greengenes" = "greengenes", "RDP"= "rdp")
else if(json_data[[1]]$type == "23S_28S" || json_data[[1]]$type == "18S") db_choices = c("Silva" = "silva","RDP"= "rdp")
if(json_data$type == "16S") db_choices = c("Silva" = "silva","Greengenes" = "greengenes", "RDP"= "rdp")
else if(json_data$type == "23S_28S" || json_data$type == "18S") db_choices = c("Silva" = "silva","RDP"= "rdp")
else db_choices = c("Findley" = "findley", "Underhill"= "underhill", "Unite"= "unite", "RDP"= "rdp")
#build_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_annotation.tsv",sep= .Platform$file.sep)
res[[1]] = fluidRow(
......@@ -65,7 +65,7 @@ Project_box_result <- function(masque_key,curdir){
shinydashboard::valueBox(ap$Count[5],tags$strong(tags$h5("Number of OTU", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("otu_icon"))
),
#column(width=5, div(img(src = "masque.png",width = "50%",height = "20%"))),
if(json_data[[1]]$type == "16S"){
if(json_data$type == "16S"){
column(width=5,
strong(h3("16S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
......@@ -73,14 +73,14 @@ Project_box_result <- function(masque_key,curdir){
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data[[1]]$type == "18S"){
else if(json_data$type == "18S"){
column(width=5,
strong(h3("18S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data[[1]]$type == "23S_28S"){
else if(json_data$type == "23S_28S"){
column(width=5,
strong(h3("23S/28S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
......@@ -121,7 +121,6 @@ Project_box_result <- function(masque_key,curdir){
)
} else{res =HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4>Result can not be shown...</h4> </em> </center>')}
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_build.tsv",sep= .Platform$file.sep)
if(file.exists(build_process))
{
......
......@@ -352,10 +352,10 @@ body <- dashboardBody(
),
box(id="box-match",title=" Match the paired files (only for paired-end sequencing)",width = NULL, status = "primary",
column(width=6, textInput("R1files",label = "Suffix R1 (Forward)",value = "_R1"),
column(width=6, textInput("R1files",label = "Suffix R1 (Forward, do not include file extension)",value = "_R1"),
selectInput("R1filesList",label = "","",multiple =TRUE,selectize=FALSE)),
column(width=6,
textInput("R2files",label = "Suffix R2 (Reverse)",value = "_R2"),
textInput("R2files",label = "Suffix R2 (Reverse, do not include file extension)",value = "_R2"),
selectInput("R2filesList",label = "","",multiple =TRUE,selectize=FALSE)
),
column(width=12,
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment