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Commit 7026a73d authored by svolant's avatar svolant
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modif selection dossier

parent 868c392d
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Rfunctions/Data_Management.R
View file @ 7026a73d
......@@ -249,10 +249,10 @@ CheckMasque <- function(input,values)
}
## At least one fastq is detected
if(is.null(Error) && input$LoadFiles>0 && length(values$fastq_names_only)==0){
Error = "<h6><strong>The selected directory must contain at least one file in the following format : fastq, fastq.gz, or fq.</strong></h6>"
HowTo = "<h6><strong>Change the working directory and check the format of the files</strong></h6>"
}
# if(is.null(Error) && input$LoadFiles>0 && length(values$fastq_names_only)==0){
# Error = "<h6><strong>The selected directory must contain at least one file in the following format : fastq, fastq.gz, or fq.</strong></h6>"
# HowTo = "<h6><strong>Change the working directory and check the format of the files</strong></h6>"
# }
if(is.null(Error) && input$PairedOrNot=='y' && input$MatchFiles_button>0){
if(length(values$R2fastQ) !=length(values$R2fastQ)){
......
server.R
View file @ 7026a73d
......@@ -30,7 +30,7 @@ shinyServer(function(input, output,session) {
## Reactive target
values <- reactiveValues(TargetWorking = target,labeled=NULL,fastq_names_only=NULL,R1fastQ=NULL,R2fastQ=NULL,
json_name=json_name,num=0,pass=pass,login_email = NULL,is.valid =NULL,
biom_masque = NULL,tree_masque=NULL,masque_key = NULL)
biom_masque = NULL,tree_masque=NULL,masque_key = NULL,paths_fastq_tmp=NULL)
## Counts file
dataInputCounts <-reactive({
......@@ -663,23 +663,38 @@ shinyServer(function(input, output,session) {
#############################################################
## Select a folder (for MASQUE)
shinyDirChoose(input, 'dir', roots = c(dir=""),filetypes = c('', 'fastq','gz','fgz'))
dir <- reactive(input$dir)
output$dirSel <- renderText({
home <- normalizePath("~")
home <- ""
path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
})
# output$dirSel <- renderText({
# print(input$dir2)
# home <- normalizePath("~")
# home <- ""
# path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# })
#
path <- reactive({
observeEvent(input$dir,{
inFiles <- input$dir
home <- normalizePath("~")
home <- ""
file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep),"*.f*q*")
if (!is.null(inFiles)){
# values$fastq_names_only = unique(paste(values$fastq_names_only,inFiles$name))
values$paths_fastq_tmp = rbind(isolate(values$paths_fastq_tmp),inFiles)
values$fastq_names_only = isolate(unique(values$paths_fastq_tmp[,"name"]))
}
})
#
# path <- reactive({
#
# home <- normalizePath("~")
# home <- ""
# file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep),"*.f*q*")
# })
CreateFasta <- reactive({
seq = NULL
......@@ -706,7 +721,7 @@ shinyServer(function(input, output,session) {
tmp = tempdir()
home <- normalizePath("~")
home <- ""
path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
## Paired-end
......@@ -720,9 +735,18 @@ shinyServer(function(input, output,session) {
if(dir.exists(pathToR1)){file.remove(list.files(pathToR1,full.names =TRUE))} else dir.create(pathToR1)
if(dir.exists(pathToR2)){file.remove(list.files(pathToR2,full.names =TRUE))} else dir.create(pathToR2)
for(i in values$R1fastQ){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files_R1",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles, detail = "Forward fastq files...")}
for(i in values$R2fastQ){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files_R2",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles, detail = "Reverse fastq files...")}
for(i in values$R1fastQ){
ind=which(i==values$paths_fastq_tmp[,"name"])[1]
file.copy(from=values$paths_fastq_tmp[,"datapath"][ind], to=paste(tmp,"Masque_files_R1",i,sep= .Platform$file.sep))
cmp = cmp +1
incProgress(cmp/nfiles, detail = "Forward fastq files...")
}
for(i in values$R2fastQ){
ind=which(i==values$paths_fastq_tmp[,"name"])[1]
file.copy(from=values$paths_fastq_tmp[,"datapath"][ind], to=paste(tmp,"Masque_files_R2",i,sep= .Platform$file.sep))
cmp = cmp +1
incProgress(cmp/nfiles, detail = "Reverse fastq files...")
}
})
} else{
......@@ -736,7 +760,9 @@ shinyServer(function(input, output,session) {
if(dir.exists(pathTo)){file.remove(list.files(pathTo,full.names =TRUE))} else dir.create(pathTo)
for(i in values$fastq_names_only){file.copy(from=paste(path_glob,i,sep=.Platform$file.sep), to=paste(tmp,"Masque_files",sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles)}
for(i in values$fastq_names_only){
ind=which(i==values$paths_fastq_tmp[,"name"])[1]
file.copy(from=values$paths_fastq_tmp[,"datapath"][ind], to=paste(tmp,"Masque_files",i,sep= .Platform$file.sep));cmp = cmp +1;incProgress(cmp/nfiles)}
})
}
......@@ -760,39 +786,40 @@ shinyServer(function(input, output,session) {
## FastQ list
output$FastQList_out <- renderUI({
FastqLoad()
NullBox = h3(strong("0 FastQ file detected"),style="color:red; text-align: center")
res = NullBox
if(length(values$fastq_names_only)>0)
{
res =list(selectInput("FastQList",label = "List of the fastq files in the selected directory",values$fastq_names_only,multiple =TRUE,selectize=FALSE,size = 6),
actionButton("RemoveFastQbut",'Remove file(s)',icon=icon("remove")))
} else res = NullBox
res = NULL
if(!is.null(input$dir)){
NullBox = h3(strong("0 FastQ file detected"),style="color:red; text-align: center")
res = NullBox
if(length(values$fastq_names_only)>0)
{
res =list(selectInput("FastQList",label = "List of the fastq files in the selected directory",isolate(values$fastq_names_only),multiple =TRUE,selectize=FALSE,size = 6),
actionButton("RemoveFastQbut",'Remove file(s)',icon=icon("remove")))
} else res = NullBox
}
return(res)
})
FastqLoad <- reactive({
input$LoadFiles
## Reinitializing
if(!is.null(isolate(values$fastq_names_only))) values$fastq_names_only = NULL
## Get the fastq names
home <- normalizePath("~")
home <- ""
path_glob = file.path(home, paste(unlist(isolate(dir()$path[-1])), collapse = .Platform$file.sep))
fastq_names = Sys.glob(isolate(path()))
if(length(fastq_names)>0 && isolate(input$LoadFiles>0))
{
if(is.null(isolate(values$fastq_names_only)) || length(isolate(values$fastq_names_only))==0) values$fastq_names_only = gsub(pattern = path_glob,x = fastq_names,replacement = "")
}
})
#
# FastqLoad <- reactive({
# input$LoadFiles
# ## Reinitializing
# if(!is.null(isolate(values$fastq_names_only))) values$fastq_names_only = NULL
#
#
# ## Get the fastq names
# home <- normalizePath("~")
# home <- ""
# # path_glob = file.path(home, paste(unlist(isolate(dir()$path[-1])), collapse = .Platform$file.sep))
#
# fastq_names = Sys.glob(isolate(path()))
#
# if(length(fastq_names)>0 && isolate(input$LoadFiles>0))
# {
# if(is.null(isolate(values$fastq_names_only)) || length(isolate(values$fastq_names_only))==0) values$fastq_names_only = gsub(pattern = path_glob,x = fastq_names,replacement = "")
# }
#
# })
## Remove FastQ function
......@@ -802,6 +829,7 @@ shinyServer(function(input, output,session) {
{
ind = which(values$fastq_names_only%in% input$FastQList)
values$fastq_names_only = values$fastq_names_only[-ind]
values$paths_fastq_tmp = values$paths_fastq_tmp[-ind,]
updateSelectInput(session, "FastQList","List of the fastq files in the selected directory",values$fastq_names_only)
}
})
......@@ -1056,12 +1084,12 @@ shinyServer(function(input, output,session) {
output$infoBoxFastQ <- renderInfoBox({
FastqLoad()
# FastqLoad()
res = NULL
res = infoBox("Fastq files","Load the fastq files ", color = "light-blue",width=NULL,icon = icon("play"),fill = TRUE)
if(input$LoadFiles>=1){
if(length(unique(values$fastq_names_only))==0) res = infoBox("Fastq files","Select a working directory with at least one fastq file", color = "red",width=NULL,icon = icon("play"),fill = TRUE)
if(!is.null(input$dir)){
if(length(unique(values$fastq_names_only))==0) res = infoBox("Fastq files","Select at least one fastq file", color = "red",width=NULL,icon = icon("play"),fill = TRUE)
if(length(unique(values$fastq_names_only))>0) res = infoBox("Fastq files",paste(length(unique(values$fastq_names_only)), "files are loaded"), color = "green",width=NULL,icon = icon("play"),fill = TRUE)
}
return(res)
......@@ -1112,7 +1140,6 @@ shinyServer(function(input, output,session) {
Error = CMP$Error
if(is.null(Error) && isolate(values$num)<100){
values$num = isolate(values$num)*100
progress_file = paste(curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_name)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
if(file.exists(progress_file))
{
......@@ -1463,17 +1490,11 @@ shinyServer(function(input, output,session) {
textMASQUE <- reactive({
samp = SamplesMasque(input,values)
home <- normalizePath("~")
home <- ""
path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# text ='<h4><b>Summary of your analysis:</b></h4> <hr color="white">'
text = paste("<b>Type of data:</b>",input$DataTypeMasque,"<br /> <br /> ",
"<b>Paired-end sequencing:</b>",input$PairedOrNot)
text = paste(text,"<br /> <br /> ","<b>Number of samples:</b>",length(samp$samples))
text = paste(text,"<br /> <br /> ","<b>Removed samples:</b>",length(samp$samples_removed))
text = paste(text,"<br /> <br /> ","<b>Working directory:</b>",path_glob)
if(isValidEmail(input$to)) text = paste(text,"<br /> <br /> ","<b>Email:</b>",input$to)
......
ui.R
View file @ 7026a73d
......@@ -236,9 +236,7 @@ body <- dashboardBody(
img_src="helpPopPup/GetKey_button.png")
),
column(width=3,
withPopup(infoBoxOutput("infoBoxFastQ",width=NULL),
title="Once you have selected your working directory you must click on this button:",
img_src="helpPopPup/LoadFiles_button.png",width_img = "60%",height_img = "60%")
infoBoxOutput("infoBoxFastQ",width=NULL)
),
column(width=3,
infoBoxOutput("infoBoxFastQ_match",width=NULL)
......@@ -339,19 +337,19 @@ body <- dashboardBody(
),
box(title="Directory containing the FastQ files ",width = NULL, status = "primary",
column(width=12,verbatimTextOutput("dirSel")),
br(),
# column(width=12,verbatimTextOutput("dirSel")),
# br(),
column(width=12,
shinyDirButton("dir", "Select a directory", "Upload",buttonType = "primary"),
HTML("&nbsp;"),
actionButton("LoadFiles",'Load',icon=icon("play"))
),
conditionalPanel(condition="input.LoadFiles>=1",
br(),
hr(),
br(),
column(width=12,uiOutput("FastQList_out"))
)
fileInput("dir",label = 'Select your fastq files',accept = c(".fastq,.fastq.gz,.fgz,.gz"),multiple = TRUE),
# shinyDirButton("dir", "Select a directory", "Upload",buttonType = "primary")
# tags$input(id = "dir2", webkitdirectory = TRUE, type = "file", onchange="pressed()"),
# HTML("&nbsp;"),
# actionButton("LoadFiles",'Load',icon=icon("play"))
uiOutput("FastQList_out")
)
),
box(id="box-match",title=" Match the paired files (only for paired-end sequencing)",width = NULL, status = "primary",
......
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