# HG changeset patch
# User ecology
# Date 1727442091 0
# Node ID 672e25c2c8c81ce0b61ba51ec272a8bd84b9c6ba
# Parent  c223db6625c13e43ddc99ec16526dbb99e84e598
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 4b040fe7867d965fb88ce70cc08081367b62b063

diff -r c223db6625c1 -r 672e25c2c8c8 eml_validate.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eml_validate.R	Fri Sep 27 13:01:31 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,"")
+} 
diff -r c223db6625c1 -r 672e25c2c8c8 test-data/report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.txt	Fri Sep 27 13:01:31 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 )."