Merge pull request #22 from maxplanck-ie/develop

added SE data and bam entry to RNAseq

app.R

@@ -185,7 +185,7 @@ server <- function(input, output, session) {
 
            else if(values$inWorkflow=="RNA-seq"){
 
-             values$command<-sprintf("mkdir -p %s ; %s ; %s ; %s --mode alignment -i %s -o %s --DE %s %s ",indir,link_cmd,cp_sInfo_cmd,path_to_exec,indir,outdir,values$sInfo_in,values$genome) 
+             values$command<-sprintf("mkdir -p %s ; %s ; %s ; %s --mode alignment -i %s -o %s --DE %s %s %s ",indir,link_cmd,cp_sInfo_cmd,path_to_exec,indir,outdir,values$sInfo_in,fbam[input$selectformat],values$genome) 
              output$command<-renderText({ values$command })
 
            } #end of RNA-seq
@@ -295,7 +295,8 @@ server <- function(input, output, session) {
         checkboxInput(inputId="fbam", label="I want to start the analysis from the bam files.", value = FALSE, width = NULL),
         checkboxInput(inputId="merge", label="I want to request sample merging.", value = FALSE, width = NULL),
         checkboxInput(inputId="beff", label="I expect batch effect in my data.", value = FALSE, width = NULL),
-        checkboxInput(inputId="nodiff", label="I don't need differential analysis.", value = FALSE, width = NULL)
+        checkboxInput(inputId="nodiff", label="I don't need differential analysis.", value = FALSE, width = NULL),
+        checkboxInput(inputId="SE", label="I have single end, NOT paired end data.", value = FALSE, width = NULL)
       )})
 
              observeEvent(input$savesubmit, {
@@ -310,13 +311,14 @@ server <- function(input, output, session) {
                merge_request<-ifelse(isolate(input$merge),"I want to request sample merging. Please consider the information I entered in the Merge column of the sample sheet. \n Please update the sample sheet after merging files.","No sample merging is needed.")
                b_eff_request<-ifelse(isolate(input$beff),"I expect batch effect in my data.","No batch effect is expected.")
                nodiff_request<-ifelse(isolate(input$nodiff),"I don't need differential analysis.","I want to request differential analysis.")
+               SE_request<-ifelse(isolate(input$nodiff),"I have single end data.","I have paired end data.")
                cc<-isolate(input$sender)
                #from<-sprintf("<sendmailR@%s>", Sys.info()[4])
                from<-"sendmailR@ie-freiburg.mpg.de"
                to<-"bioinfo-core@ie-freiburg.mpg.de" 
                #to<-"sikora@ie-freiburg.mpg.de"
                subject<-paste0("Analysis request ",isolate(input$analysistitle), "_" ,isolate(values$ranstring))
-               msg <- gsub(";","\n \n",paste0(cc," has requested the following analysis: \n \n Workflow: ", isolate(values$inWorkflow)," \n \n Genome: ", values$genome," \n \n ", fbam_request, " \n \n " ,merge_request," \n \n ", b_eff_request ," \n \n ", nodiff_request," \n \n User comments: \n \n", isolate(input$comments),"\n \n Please review the input files and the attached sample sheet before proceeding. \n \n End of message. \n \n ",paste(rep("#",times=80),collapse="")," \n \n ", values$command ,"\n \n"))
+               msg <- gsub(";","\n \n",paste0(cc," has requested the following analysis: \n \n Workflow: ", isolate(values$inWorkflow)," \n \n Genome: ", values$genome," \n \n ", fbam_request, " \n \n " ,merge_request," \n \n ", b_eff_request ," \n \n ", nodiff_request, " \n \n ", SE_request," \n \n User comments: \n \n", isolate(input$comments),"\n \n Please review the input files and the attached sample sheet before proceeding. \n \n End of message. \n \n ",paste(rep("#",times=80),collapse="")," \n \n ", values$command ,"\n \n"))
                if(values$inWorkflow=="ChIP-seq"){
                  sendmail(from=sprintf("%s",from), to=to, subject=subject, control=list(smtpServer="owa.ie-freiburg.mpg.de"), msg=list(msg,mime_part(isolate(values$sInfoDest)),mime_part(isolate(values$chDictDest)),mime_part(bshscript)),cc=sprintf("%s",cc))
                }