Add radio button gestion and dl pipeline

main.R

 source("tools.R")
 library(yaml)
 
-path_yml <- "/home/mbb/Documents/sag/pipeline.yml"
+path_yml <- "/home/mbb/Documents/waw/workflows/RNAseq/sag.yaml"
 
 path_tools <- "/home/mbb/Documents/sag/predefined_tools/"
 
@@ -425,8 +425,8 @@ generate_pages_server <- function() {
       if(length(boxes) > 0) {
         
         
-        #resG <- resG + '\t\tres <- paste(res, "outil_' + APP$pages[[x]]$name + '_' + panel$name + ':", paste0(\'\"\', input$select' + panel$name + ', \'\"\'), "\\n", sep = " ")\n'
-        resG <- resG + '\t\tres <- paste(res, "'+APP$pages[[x]]$name + ':", paste0(\'\"\', input$select' + APP$pages[[x]]$name + ', \'\"\'), "\\n", sep = " ")\n'
+        #resG <- resG + '\t\tres = res + paste("outil_' + APP$pages[[x]]$name + '_' + panel$name + ':", paste0(\'\"\', input$select' + panel$name + ', \'\"\'), "\\n", sep = " ")\n'
+        resG <- resG + '\t\tres = res + paste("'+APP$pages[[x]]$name + ':", paste0(\'\"\', input$select' + APP$pages[[x]]$name + ', \'\"\'), "\\n", sep = " ")\n'
         for(b in 1:length(boxes)) {  # list boxes
           
           box <- boxes[[b]]
@@ -463,36 +463,36 @@ generate_pages_server <- function() {
             
               if(type == 'text') {
                   genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
-                  genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", input$' + id + ', "\\n", sep = " ")\n'
+                  genR <-  genR + '\t\t\tres = res + paste("' + id + ':", input$' + id + ', "\\n", sep = " ")\n'
                   genR <-  genR + '\t\t} else {\n'
-                  genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " ")\n'
+                  genR <-  genR + '\t\t\tres = res + paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " ")\n'
                   genR <-  genR + '\t\t}'
                   genR <-  genR + '\t\n\n'
               } else if(cnt$type == "slider") {
                 if(length(cnt$value) == 1) {
-                  genR <-  genR + '\t\tres <- paste(res, "' + id + ':", input$' + id + ', "\\n", sep = " ")'
+                  genR <-  genR + '\t\tres = res + paste("' + id + ':", input$' + id + ', "\\n", sep = " ")'
                   genR <-  genR + '\t\n\n'
                 } else {
-                  genR <-  genR + '\t\tres <- paste(res, "' + id + '_min:", input$' + id + '[1], "\\n", sep = " ")\n'
-                  genR <-  genR + '\t\tres <- paste(res, "' + id + '_max:", input$' + id + '[2], "\\n", sep = " ")\n'
-                  genR <-  genR + '\t\tres <- paste(res, "' + id + '_step:", "' + cnt$step + '", "\\n", sep = " ")\n'
+                  genR <-  genR + '\t\tres = res + paste("' + id + '_min:", input$' + id + '[1], "\\n", sep = " ")\n'
+                  genR <-  genR + '\t\tres = res + paste("' + id + '_max:", input$' + id + '[2], "\\n", sep = " ")\n'
+                  genR <-  genR + '\t\tres = res + paste("' + id + '_step:", "' + cnt$step + '", "\\n", sep = " ")\n'
                   genR <-  genR + '\t\n\n'
                 }
               } else if(cnt$type == "select") {
                 genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
-                genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", input$' + id + ', "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", input$' + id + ', "\\n", sep = " ")\n'
                 genR <-  genR + '\t\t} else {\n'
-                genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " ")\n'
                 genR <-  genR + '\t\t}'
                 genR <-  genR + '\t\n\n'
               } else if(cnt$type == "file") {
-                genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", paste0(\'\"\', input$' + id + '$datapath, \'\"\'), "\\n", sep = " ")'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", paste0(\'\"\', input$' + id + '$datapath, \'\"\'), "\\n", sep = " ")'
                 genR <-  genR + '\t\n\n'
               } else if(cnt$type == "checkbox") {
                 genR <-  genR + '\t\tif(input$' + id + ') {\n'
-                genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", "true", "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", "true", "\\n", sep = " ")\n'
                 genR <-  genR + '\t\t} else {\n'
-                genR <-  genR + '\t\t\tres <- paste(res, "' + id + ':", "false", "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", "false", "\\n", sep = " ")\n'
                 genR <-  genR + '\t\t}'
                 genR <-  genR + '\t\n\n'
               } else if(cnt$type == "chooser") {
@@ -520,8 +520,16 @@ generate_pages_server <- function() {
                 genR <-  genR + '\t\t}		\n'
                 genR <-  genR + '\t\tres <- paste0(res, "]", "\\n")\n\n'
                 
-                
-              } else {
+              } else if(cnt$type == "radio") {
+                genR <-  genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", input$' + id + ', "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t} else {\n'
+                genR <-  genR + '\t\t\tres = res + paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " ")\n'
+                genR <-  genR + '\t\t}'
+                genR <-  genR + '\t\n\n'
+              }
+              
+              else {
                 #TODO
               }
               
@@ -633,20 +641,16 @@ generate_pages_server <- function() {
   
   res <- res + resG # Add content
 
-  res <- res + 'setwd(path_param)\n'
+  res <- res + '\tsetwd(path_param)\n'
   
   res <- res + '\twrite(res, file="params.yml")\n'
 
-  res <- res + 'fs = c("params.yml")\n'
-
-  # generate snakefile
-  res <- res + ''
-
-  # generate container file
-  res <- res + ''
+  res <- res + '\tsystem("python3 /home/mbb/Documents/waw/main.py",wait=TRUE)\n'
+	res <- res + '\tsetwd("/home/mbb/Documents/waw")\n'
+	res <- res + '\tfs = c("Snakefile","params.total.yml","recipe.singularity","report.rmd")\n'
 
   # create zip file
-  res <- res + 'zip(zipfile=file, files=fs)\n'
+  res <- res + '\tzip(zipfile=file, files=fs)\n'
   res <- res + '},\n'
   res <- res + 'contentType = "application/zip"\n'