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annotate make_eml.R @ 0:e6d531c277f6 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
author ecology
date Sat, 02 Dec 2023 01:50:16 +0000
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0
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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1 ##07/06/2023 ##Genthon Tanguy
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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2 ##update 15/11/2023 ##Seguineau Pauline
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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3
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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4 ###make_eml
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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5
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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6 args = commandArgs(trailingOnly=TRUE)
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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7 if(length(args)>0){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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8 title <- args[1]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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9 start <- args[2]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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10 end <-args[3]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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11 data_table <- args[4]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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12 data_other <- args[5]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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13 destable <- args[6]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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14 desother <- args[7]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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15 quote <- args[8]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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16 table_url <- args[9]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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17 other_url <- args[10]
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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18 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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21 ###Format data###
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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23 if (data_table == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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24 table=NULL
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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25 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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26 table = strsplit(data_table," ")
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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27 for (file in table){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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28 name_table = gsub("\\.[a-zA-Z]*", "", file)}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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29 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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31
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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32 if (quote != ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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33 quote = strsplit(quote,",")
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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34 if (length(quote[[1]]) != length(table[[1]])){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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35 stop("Your number of quote(s) isn't equal to your number of data table file(s). Please enter the quote parameter as many time as the number of data tables you've input")}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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36 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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39 tablequote=NULL
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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40 for (quote_table in quote[[1]]){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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41 if (quote_table=="quote"){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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42 quote_table = sub("quote",'"', quote_table)}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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43 else if (quote_table=="apostrophe"){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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44 quote_table = gsub("apostrophe","'",quote_table)}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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45 else if (quote_table=="none"){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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46 quote_table = gsub("none","",quote_table)}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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47 tablequote = c(tablequote, quote_table)
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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48 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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49
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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51 if (data_other == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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52 other=NULL
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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53 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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54 other = strsplit(data_other," ")
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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55 for (file in other){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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56 name_other = gsub("\\.[a-zA-Z]*", "", file)}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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57 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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58
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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59 if (data_table !=""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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60 if (destable == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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61 des_table = name_table
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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62 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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63 des_table = strsplit(destable,",")}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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64 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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67 if (data_other !=""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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68 if (desother == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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69 des_other = name_other
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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70 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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71 des_other = strsplit(desother,",")}
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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72 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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75 if (data_table !=""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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76 if (table_url == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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77 urltable = ""
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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78 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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79 table_url = gsub("\\-" ,"", table_url)
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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80 urltable = strsplit(table_url,",")
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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81 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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82 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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83
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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84 if (data_other !=""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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85 if (other_url == ""){
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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86 urlother = ""
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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87 }else{
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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88 other_url = gsub("\\-" ,"", other_url)
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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89 urlother = strsplit(other_url,",")
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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90 }
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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91 }
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92
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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93 ###Make EML###
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94
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95 if (!is.null(table) && !is.null(other)){
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96
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97 EMLassemblyline::make_eml(
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98 path="output_template",
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99 data.path="data_files",
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100 eml.path=".",
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101 dataset.title = title,
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102 temporal.coverage = c(start,end),
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103 data.table=table[[1]],
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104 data.table.name = name_table,
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ecology
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105 data.table.description = des_table[[1]],
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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106 data.table.quote.character = tablequote,
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
ecology
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107 data.table.url = urltable[[1]],
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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108 other.entity=other[[1]],
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109 other.entity.name = name_other,
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ecology
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110 other.entity.description = des_other[[1]],
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111 other.entity.url= urlother[[1]]
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ecology
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112 )
e6d531c277f6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
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113
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114 }else if (is.null(table) && is.null(other)){
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115
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116 EMLassemblyline::make_eml(
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117 path="output_template",
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118 data.path="data_files",
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119 eml.path=".",
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120 dataset.title = title,
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121 temporal.coverage = c(start,end))
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122
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123 }else if (!is.null(table) && is.null(other)){
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124
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125 EMLassemblyline::make_eml(
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126 path="output_template",
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127 data.path="data_files",
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128 eml.path=".",
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129 dataset.title = title,
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130 temporal.coverage = c(start,end),
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131 data.table=table[[1]],
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132 data.table.name = name_table,
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133 data.table.description = des_table[[1]],
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134 data.table.quote.character = tablequote,
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135 data.table.url = urltable[[1]])
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136
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137
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138 }else if (is.null(table) && !is.null(other)){
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139
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140 EMLassemblyline::make_eml(
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141 path="output_template",
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142 data.path="data_files",
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143 eml.path=".",
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144 dataset.title = title,
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145 temporal.coverage = c(start,end),
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146 other.entity=other[[1]],
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147 other.entity.name = name_other,
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148 other.entity.description = des_other[[1]],
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149 other.entity.url= urlother[[1]])}
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150
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151
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152
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153 old.names <- list.files(path=".", pattern=".xml")
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154 print(old.names)
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155 file.rename(from=old.names, to="eml.xml")
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156
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157
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158
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159
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160
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161