Mercurial > repos > ecology > annotations_template
changeset 1:dbba9bedd4bd draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063
| author | ecology |
|---|---|
| date | Fri, 27 Sep 2024 13:00:18 +0000 |
| parents | fab3ca90cb26 |
| children | |
| files | eml_validate.R test-data/report.txt |
| diffstat | 2 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eml_validate.R Fri Sep 27 13:00:18 2024 +0000 @@ -0,0 +1,35 @@ +#17/09/2024 +#Seguineau Pauline + +#EML validate + +#Load packages + +library(emld) +library(EML) + +#Load arguments + +args = commandArgs(trailingOnly=TRUE) + +if(length(args)>0){ + eml_file <- args[1] +}else{ + +stop("This tool needs at least one argument.")} + +#run eml_validate + +eml = read_eml(eml_file) + +eml_valid = eml_validate(eml) + +if(eml_valid==T){ + cat("Your EML is valid.") +}else if(eml_valid==F && length(attr(eml_valid,""))>1){ + cat("Your EML is not valid. You can improve it by correcting these errors:","\n") + attr(eml_valid,"") +}else{ + cat("Your EML is not valid. You can improve it by correcting this error:","\n") + attr(eml_valid,"") +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.txt Fri Sep 27 13:00:18 2024 +0000 @@ -0,0 +1,2 @@ +Your EML is not valid. You can improve it by correcting this error: +[1] "Element 'creator': This element is not expected. Expected is one of ( references, alternateIdentifier, shortName, title )."