if(input$PairedOrNot=='y')HowTo='<h6><strong>Make sur that you click the « Load » button. <br /> Change the working directory and/or verify the pairs matching.</strong></h6>'
if(input$PairedOrNot=='n')HowTo='<h6><strong>Make sur that you click the « Load » button. <br /> Change the working directory.</strong></h6>'
if(input$PairedOrNot=='y')HowTo='<h6><strong>Make sure that you click the « Match » button. <br /> Change the working directory and/or verify the pairs matching.</strong></h6>'
if(input$PairedOrNot=='n')HowTo='<h6><strong>Make sure that your samples have the correct extension (.fastq, .fq, .fastq.gz or .fq.gz). <br /> Change the working directory.</strong></h6>'
HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em><br/> </center>'),
#HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em><br/> </center>'),
HTML('<center><h1><strong>Your project is done !</strong></h1></center>'),
br(),
column(width=5,
valueBox(ap$Count[1],tags$strong(tags$h5("Number of amplicons",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("amplicon_icon")),
valueBox(ap$Count[2],tags$strong(tags$h5("Remaining amplicons after dereplication",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("dereplication_icon")),
valueBox(ap$Count[3],tags$strong(tags$h5("Remaining amplicons after removing singletons",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("singleton_icon")),
valueBox(ap$Count[4],tags$strong(tags$h5("Remaining amplicons after removing chimera",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("chimera_icon"))
column(width=4,
h3("OTU building process"),
shinydashboard::valueBox(ap$Count[1],tags$strong(tags$h5("Number of amplicons",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("amplicon_icon")),
shinydashboard::valueBox(ap$Count[2],tags$strong(tags$h5("Remaining amplicons after dereplication",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("dereplication_icon")),
shinydashboard::valueBox(ap$Count[3],tags$strong(tags$h5("Remaining amplicons after removing singletons",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("singleton_icon")),
shinydashboard::valueBox(ap$Count[4],tags$strong(tags$h5("Remaining amplicons after removing chimera",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("chimera_icon")),
shinydashboard::valueBox(ap$Count[5],tags$strong(tags$h5("Number of OTU",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("otu_icon"))
),
column(width=5,offset=2,
box(title="Upload the results",width=NULL,background="light-blue",
selectInput("masque_database","Select the database",choices=c("Silva"="silva","Greengenes"="greengenes")),
shinydashboard::valueBox(ap$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$Count[7],tags$strong(tags$h5("Number of OTU annotated by Greengenes",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("greengenes_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("rdp_icon"))
)
}
elseif(json_data[[1]]$type=="23S_28S"){
column(width=5,
strong(h3("23S/28S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by RDP",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("rdp_icon"))
)
}
else{
column(width=5,
strong(h3("ITS annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by Unite",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("unite_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Findley",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("findley_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by Underhill",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("underhill_icon")),
shinydashboard::valueBox(ap$Count[9],tags$strong(tags$h5("Number of OTU annotated by RDP",style="width: 70%;")),color="light-blue",width=NULL,icon=uiOutput("rdp_icon"))
)
},
#offset = 4,
column(width=3,
strong(h3("Start statistical analysis")),
box(title="Load the results",width=NULL,background="light-blue",
selectInput("masque_db","Select the database",choices=db_choices),
}else{res=HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4>Result can not be shown...</h4> </em> </center>')}
}else{res=HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em> </center>')}
HTML('<center><h1><strong>Sorry, the workflow failed during progression</strong></h1> <br/> <em><h4> Hereafter is the message error.</h4> </em> <br/> </center>'),
HTML('<center><h1><strong>The workflow failed during progression</strong></h1> <br/> </center>'),