diff make_eml.R @ 0:5bfceb4ef59b draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_eml.R	Sat Dec 23 20:40:51 2023 +0000
@@ -0,0 +1,442 @@
+##07/06/2023 ##Genthon Tanguy
+##update 15/11/2023 ## Seguineau Pauline
+
+###make_eml
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  title <- args[1]
+  start <- args[2]
+  end <-args[3]
+  data_table <- args[4]
+  data_raster <- args[5]
+  data_vector <- args[6]
+  data_other <- args[7]
+  destable <- args[8]
+  desraster<- args[9]
+  desvector<- args[10]
+  desother <- args[11]
+  quote <- args[12]
+  table_url <- args[13]
+  other_url <- args[14]
+  raster_url <- args[15]
+  vector_url <- args[16]
+}
+
+#Load package
+
+library(EMLassemblyline)
+sessionInfo()
+
+
+###Format data###
+if (data_table == ""){
+    table=NULL
+}else{
+    table =  strsplit(data_table," ")
+    for (file in table){
+         name_table = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+    
+    
+if (quote != ""){
+   quote = strsplit(quote,",")
+   if (length(quote[[1]]) != length(table[[1]])){
+   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")}
+}
+
+
+tablequote=NULL
+for (quote_table in quote[[1]]){
+    if (quote_table=="quote"){
+        quote_table = sub("quote",'"', quote_table)}
+    else if (quote_table=="apostrophe"){
+             quote_table = gsub("apostrophe","'",quote_table)}
+    else if (quote_table=="none"){
+             quote_table = gsub("none","",quote_table)}
+    tablequote = c(tablequote, quote_table)
+}
+
+  
+if (data_raster == ""){
+    raster=NULL
+}else{
+    raster =  strsplit(data_raster," ")
+    for (file in raster){
+         name_raster = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+    
+if (data_vector == ""){
+    vector=NULL
+}else{
+    vector =  strsplit(data_vector," ")
+    for (file in vector){
+         name_vector = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+
+if (data_other == ""){
+    other=NULL
+}else{
+    other =  strsplit(data_other," ")
+    for (file in other){
+         name_other = gsub("\\.[a-zA-Z]*", "", file)}
+         }
+
+if (data_table !=""){
+   if (destable == ""){
+       des_table = name_table
+   }else{
+       des_table =  strsplit(destable,",")}
+}
+
+if (data_raster !=""){
+   if (desraster == ""){
+       des_raster = name_raster
+   }else{
+       des_raster =  strsplit(desraster,",")}
+}
+
+if (data_vector !=""){ 
+   if (desvector == ""){
+       des_vector = name_vector
+   }else{
+       des_vector =  strsplit(desvector,",")}
+}
+
+if (data_other !=""){
+   if (desother == ""){
+       des_other = name_other
+   }else{
+       des_other =  strsplit(desother,",")}
+}
+
+if (data_table !=""){
+   if (table_url == ""){
+       urltable = ""
+   }else{
+       table_url = gsub("\\-" ,"", table_url)
+       urltable =  strsplit(table_url,",")
+   }
+}
+
+if (data_other !=""){
+   if (other_url == ""){
+       urlother = ""
+   }else{
+       other_url = gsub("\\-" ,"", other_url)
+       urlother =  strsplit(other_url,",")
+   }
+}
+
+if (data_raster !=""){
+   if (raster_url == ""){
+       urlraster = ""
+   }else{
+       raster_url = gsub("\\-" ,"", raster_url)
+       urlraster =  strsplit(raster_url,",")
+   }
+}
+
+if (data_vector !=""){
+   if (vector_url == ""){
+       urlvector = ""
+   }else{
+       vector_url = gsub("\\-" ,"", vector_url)
+       urlvector =  strsplit(vector_url,",")
+   }
+}
+
+
+
+###Make EML###
+   
+if (!is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end))
+   
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]]
+                      )
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (!is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                 
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])}
+
+issues()
+old.names <- list.files(path=".", pattern=".xml")
+file.rename(from=old.names, to="eml.xml")
+
+
+
+
+
+