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annotate eml_validate.R @ 2:79f2ca0bfa9a draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 61182ba790bdeeb98750403b869051ccad1a736c
author ecology
date Thu, 16 Jan 2025 15:56:27 +0000
parents dbba9bedd4bd
children
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
ecology
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1 #17/09/2024
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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2 #Seguineau Pauline
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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4 #EML validate
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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6 #Load packages
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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8 library(emld)
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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9 library(EML)
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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11 #Load arguments
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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13 args = commandArgs(trailingOnly=TRUE)
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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15 if(length(args)>0){
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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16 eml_file <- args[1]
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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17 }else{
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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19 stop("This tool needs at least one argument.")}
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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21 #run eml_validate
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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23 eml = read_eml(eml_file)
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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25 eml_valid = eml_validate(eml)
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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27 if(eml_valid==T){
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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28 cat("Your EML is valid.")
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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29 }else if(eml_valid==F && length(attr(eml_valid,""))>1){
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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30 cat("Your EML is not valid. You can improve it by correcting these errors:","\n")
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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31 attr(eml_valid,"")
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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32 }else{
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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33 cat("Your EML is not valid. You can improve it by correcting this error:","\n")
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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34 attr(eml_valid,"")
dbba9bedd4bd planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
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35 }