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1 #!/usr/bin/env Rscript
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2 #Use a Rdata file and attributes to extract
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3 #Get every argument and write a file with its values(s)
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4
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5
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6 #get the rdata file
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7 args = commandArgs(trailingOnly=TRUE)
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8 rdata<-load(args[1])
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9 rdata<-get(rdata)
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10 sum<-summary(rdata)
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11
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12 #get the selected attributes to explore
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13 attributes_selected <- commandArgs(trailingOnly=TRUE)[2]
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14 attributes<-strsplit(attributes_selected, ",") #List of elements
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15
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16 write.table(sum,file = "summary.tabular",sep='\t',row.names=FALSE)
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17 len<-length(attributes[[1]])-1
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18 bind<-tail(args,n=1)
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19
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20 #file type definition
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21 file_ext<-function(ext){
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22 file<-paste(attributes[[1]][i],ext,sep="") #Filename definition
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23 file<-paste("outputs/",file,sep="")
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24 return(file)
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25 }
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26
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27 for (i in 1:len){
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28 attribute<-attributes[[1]][i] #Get the attribute i
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29 if(! any(names(rdata)==attribute)){
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30 error<-paste(attribute, " doesn't exist in the RData. Check the inputs files")
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31 write(error, stderr())
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32 }
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33
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34 attribute_val<-eval(parse(text=paste("rdata$",attribute,sep=""))) #Extract the value(s)
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35
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36 if(is.null(attribute_val)){ #Galaxy can't produce output if NULL
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37 file<-file_ext(".txt")
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38 write("Return NULL value",file=file)
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39 next #Exit loop
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40 }
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41
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42 if (typeof(attribute_val)=="list"){ #Need to be corrected, fail in galaxy but not in R
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43 if(length(attribute_val)=="0"){
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44 file<-file_ext(".txt")
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45 sink(file=file)
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46 print("Empty list :") #If the list is empty without element, file is empty and an error occur in galaxy
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47 print(attribute_val)
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48 sink()
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49 next
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50 }else{
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51 attribute_val<-as.data.frame(do.call(rbind, attribute_val))
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52 file<-file_ext(".tabular")
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53 write.table(attribute_val,file=file,row.names=FALSE)
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54 next
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55 }
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56 }else if (typeof(attribute_val)=="language"){ #OK
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57 attribute_val<-toString(attribute_val,width = NULL)
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58 file<-file_ext(".txt")
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59 write(attribute_val,file=file)
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60 next
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61 }
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62 file<-file_ext(".tabular")
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63 dataframe<-as.data.frame(attribute_val)
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64 names(dataframe)<-attribute
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65 if(bind=="nobind"){
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66 write.table(dataframe,file=file,row.names=FALSE,sep=" ")
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67 }else{
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68 if(!exists("alldataframe")){
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69 alldataframe<-dataframe
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70 }else{
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71 alldataframe<-cbind(alldataframe, dataframe)
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72 }
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73 }
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74 }
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75
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76 if(exists("alldataframe")&&bind=="bind"){
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77 write.table(alldataframe,file=file,row.names=FALSE,sep=" ")
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78 }
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79 q('no')
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