# HG changeset patch
# User ecology
# Date 1703364070 0
# Node ID 59349973537f91825fd40c3c8d6021e919c71e98
# Parent  642e31c435c9e4f9a3a50f6404fb60c806e2f52e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32

diff -r 642e31c435c9 -r 59349973537f entities_templates.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/entities_templates.R	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,17 @@
+#19/12/2023 #SEGUINEAU Pauline 
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+    data_objects <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+data =  strsplit(data_objects," ")[[1]]
+
+#Make entities templates for raster and/or vector and/or other entities data
+
+EMLassemblyline::template_entities(path="output_template",data.path="data_files",data.objects=data)
+
+
diff -r 642e31c435c9 -r 59349973537f geo_cov_temp.R
--- a/geo_cov_temp.R	Mon Dec 04 21:49:43 2023 +0000
+++ b/geo_cov_temp.R	Sat Dec 23 20:41:10 2023 +0000
@@ -30,6 +30,7 @@
 }else if (empty=="true"){
    empty=TRUE}
 
+
 #Make template
 
 template_geographic_coverage(path =".", data.path = "data_files", data.table = tablename, lat.col = latcol, lon.col = longcol, site.col = sitecol, empty = empty)
diff -r 642e31c435c9 -r 59349973537f make_eml.R
--- a/make_eml.R	Mon Dec 04 21:49:43 2023 +0000
+++ b/make_eml.R	Sat Dec 23 20:41:10 2023 +0000
@@ -1,5 +1,5 @@
 ##07/06/2023 ##Genthon Tanguy
-##update 15/11/2023 ##Seguineau Pauline
+##update 15/11/2023 ## Seguineau Pauline
 
 ###make_eml
 
@@ -9,17 +9,27 @@
   start <- args[2]
   end <-args[3]
   data_table <- args[4]
-  data_other <- args[5]
-  destable <- args[6]
-  desother <- args[7]
-  quote <- args[8]
-  table_url <- args[9]
-  other_url <- args[10]
+  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{
@@ -48,6 +58,22 @@
 }
 
   
+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{
@@ -63,6 +89,19 @@
        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 == ""){
@@ -71,7 +110,6 @@
        des_other =  strsplit(desother,",")}
 }
 
-
 if (data_table !=""){
    if (table_url == ""){
        urltable = ""
@@ -90,9 +128,79 @@
    }
 }
 
+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(other)){
+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",
@@ -105,22 +213,203 @@
                       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(other)){
-  
+                      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))
+                      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)){
    
-}else if (!is.null(table) && 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",
@@ -132,26 +421,18 @@
                       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(other)){
-
-   EMLassemblyline::make_eml(
-                      path="output_template",
-                      data.path="data_files",
-                      eml.path=".", 
-                      dataset.title = title,
-                      temporal.coverage = c(start,end),
+                      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")
-print(old.names)
 file.rename(from=old.names, to="eml.xml")
 
 
diff -r 642e31c435c9 -r 59349973537f make_eml.xml
--- a/make_eml.xml	Mon Dec 04 21:49:43 2023 +0000
+++ b/make_eml.xml	Sat Dec 23 20:41:10 2023 +0000
@@ -1,8 +1,7 @@
-<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0" profile="22.05">
+<tool id="makeeml" name="Make EML" version="0.1.1+galaxy1" profile="22.05">
     <description> Create EML from EAL templates</description>
     <requirements>
-        <requirement type="package" version="4.3.1">r-base</requirement>
-        <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
+        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     
@@ -18,6 +17,18 @@
         #set $table += $indata.element_identifier + " ";
     #end for
     
+    #set $raster = ""
+    #for $data_raster in $dataraster
+        ln -s '$data_raster' 'data_files/${data_raster.element_identifier}';
+        #set $raster += $data_raster.element_identifier + " ";
+    #end for
+    
+    #set $vector = ""
+    #for $data_vector in $datavector
+        ln -s '$data_vector' 'data_files/${data_vector.element_identifier}';
+        #set $vector += $data_vector.element_identifier + " ";
+    #end for
+    
     #set $other = ""
     #for $data_other in $dataother
         ln -s '$data_other' 'data_files/${data_other.element_identifier}';
@@ -29,22 +40,34 @@
        #set $quotetable += $q.quote + ",";
     #end for 
 
+    
     Rscript 
      '$__tool_directory__/make_eml.R' 2> err.txt
      '$title'
      '$temporal_coverage.start'
      '$temporal_coverage.end'
      '$table'
+     '$raster'
+     '$vector'
      '$other'
      '$destable'
+     '$desraster'
+     '$desvector'
      '$desother'
      '$quotetable'
      '$table_url'
      '$other_url'
+     '$raster_url'
+     '$vector_url'
 		
     ]]></command>
     <inputs>
-        <param name="templates" type="data_collection"  collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection with only tabular files." />
+        <param name="templates" type="data" multiple="True" label="Upload all EAL templates" help="You can upload dataset collection or upload templates one by one (especially if there are multiple format)."/>
+        <param name="title" type="text" label="Title for your dataset." />
+      <section name="temporal_coverage" title="Temporal coverage" expanded="true">
+	<param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" optional="false"/>
+	<param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" optional="false"/>
+      </section>
       <section name="data_table" title="Do you have data table ? " >
         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are data table" help= "Input a data collection." optional = "true"/>
         <param name="destable" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
@@ -57,16 +80,21 @@
         </repeat>
         <param name="table_url" type="text" label="Give the publicly accessible URL from which your data table can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
       </section>
+      <section name="data_raster" title="Do you have raster data ? " >
+        <param name="dataraster" type="data_collection"  collection_type="list"  label="Upload all data files wich are spatial raster" help= "Input a data collection." optional = "true"/>
+        <param name="desraster" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
+        <param name="raster_url" type="text" label="Give the publicly accessible URL from which your raster data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
+      </section>
+      <section name="data_vector" title="Do you have vector data ? " >
+        <param name="datavector" type="data_collection"  collection_type="list"  label="Upload all data files wich are spatial vector" help= "Input a data collection." optional = "true"/>
+        <param name="desvector" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
+        <param name="vector_url" type="text" label="Give the publicly accessible URL from which your vector data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
+      </section>
       <section name="data_other" title="Do you have other data entity ? " >
         <param name="dataother" type="data_collection"  collection_type="list"  label="Upload all data files wich are other entity" help= "Input a data collection." optional = "true"/>
-        <param name="desother" type="text" label="Give a short description of your data file. If there are multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
+        <param name="desother" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
         <param name="other_url" type="text" label="Give the publicly accessible URL from which your other data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
       </section>
-	<param name="title" type="text" label="Title for your dataset." />
-      <section name="temporal_coverage" title="Temporal coverage" >
-	<param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" />
-	<param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" />
-      </section>
     </inputs>
     <outputs>
 		 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
@@ -74,28 +102,18 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2"> 
-            <param name="templates">
-                <collection type="list">
-			<element name="annotations.txt" value="annotations.txt"/>
-                        <element name="keywords.txt" value="keywords.txt" />
-                        <element name="attributes_data_blary_al.txt" value="attributes_data_blary_al.txt"/>
-                        <element name="catvars_data_blary_al.txt" value="catvars_data_blary_al.txt"/>
-                        <element name="geographic_coverage.txt" value="geographic_coverage.txt" />
-                        <element name="personnel.txt" value="personnel.txt" />
-                </collection>
+            <param name="templates" value="annotations.txt,keywords.txt,attributes_data_blary_al.txt,catvars_data_blary_al.txt,geographic_coverage.tabular,personnel.txt" >
             </param>
             <output name="metadataout" >
-			<assert_contents>
-				<is_valid_xml />
-				<xml_element path="./dataset"/>
-                	</assert_contents>
+                <assert_contents>
+                    <is_valid_xml />
+                    <xml_element path="./dataset"/>
+                </assert_contents>
             </output>
         </test>
     </tests>
 <help><![CDATA[
-.. class:: warningmark
 
-'''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates in tabular format.
 
 **What it does?**
 --------------------
@@ -105,30 +123,17 @@
 
 **How to use it?**
 --------------------
-To use this tool, you can select, in your history a data collection with EAL templates made by the eml2eal tool. 
-You can also select your own templates that you have to integrate into a Galaxy collection.
+To use this tool, you can select, in your history a data collection with EAL templates or select templates one by one.
 
 To do so you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click
 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
 You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
 
-**Recommended optional input:**
-
-Data files : If you have data files you can input them to give more information in your metadata file. There are two parameters to do to so. The first is "Do you have data table ?" that provide you to import a collection with all your data table. The second is "Do you have other data entity ?" is for all your data file that not data table. 
-
-Description : You can add a short description of each data files you input. If there are multiple data files, please separate your descriptions with a comma (,) in the same order of your data input 
-
-Quote : If you have import data table files, you can specify if there are quotes and what type of quote is it. Repeat this parameter as many times as the number of data tables you've input and in the same order
-
-Title : You can give a title for your dataset.
-
-Temporal coverage : You can specify the temporal coverage of your data. 
-
  .. class:: infomark 
  
  Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
  
 
-You then have to select your collection in the upload box of the tool and click **Execute** to get your EML metadata.
+
 ]]></help>
 </tool>
diff -r 642e31c435c9 -r 59349973537f raster_templates.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raster_templates.R	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,22 @@
+#15/12/2023 #SEGUINEAU Pauline 
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+    data_raster <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+raster =  strsplit(data_raster," ")
+
+#Make templates to describe data raster
+
+template_raster_attributes(path = ".",data.path= "data_files", raster.file = raster[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+
+
diff -r 642e31c435c9 -r 59349973537f test-data/Present_Surface_pH.tif
Binary file test-data/Present_Surface_pH.tif has changed
diff -r 642e31c435c9 -r 59349973537f test-data/attributes_data_7.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/attributes_data_7.txt	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,7 @@
+attributeName	attributeDefinition	class	unit	dateTimeFormatString	missingValueCode	missingValueCodeExplanation
+LIB_SITE	Description for: LIB_SITE	character	""	""	""	""
+X	Description for: X	numeric	dimensionless	""	""	""
+Y	Description for: Y	numeric	dimensionless	""	""	""
+PROGRAMME	Description for: PROGRAMME	categorical	""	""	""	""
+OPERATEUR_	Description for: OPERATEUR_	categorical	""	""	""	""
+STATUT_DU_	Description for: STATUT_DU_	categorical	""	""	""	""
diff -r 642e31c435c9 -r 59349973537f test-data/catvars_data_7.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/catvars_data_7.txt	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,13 @@
+attributeName	code	definition
+PROGRAMME	DCE	Value: DCE for attribute: PROGRAMME
+PROGRAMME	ELV	Value: ELV for attribute: PROGRAMME
+PROGRAMME	DCE/ELV	Value: DCE/ELV for attribute: PROGRAMME
+PROGRAMME	REBENT	Value: REBENT for attribute: PROGRAMME
+PROGRAMME	REBENT/DCE	Value: REBENT/DCE for attribute: PROGRAMME
+OPERATEUR_	MNHN CC	Value: MNHN CC for attribute: OPERATEUR_
+OPERATEUR_	Station de Wimer	Value: Station de Wimer for attribute: OPERATEUR_
+OPERATEUR_	Ifremer Anglet	Value: Ifremer Anglet for attribute: OPERATEUR_
+OPERATEUR_	Bio-Littoral	Value: Bio-Littoral for attribute: OPERATEUR_
+OPERATEUR_	Ecosub	Value: Ecosub for attribute: OPERATEUR_
+STATUT_DU_	actif	Value: actif for attribute: STATUT_DU_
+STATUT_DU_	inactif	Value: inactif for attribute: STATUT_DU_
diff -r 642e31c435c9 -r 59349973537f test-data/custom_units.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_units.txt	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,1 @@
+id	unitType	parentSI	multiplierToSI	description
diff -r 642e31c435c9 -r 59349973537f test-data/data_7.GeoJSON
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_7.GeoJSON	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,72 @@
+{
+"type": "FeatureCollection",
+"name": "shapefile",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+"features": [
+{ "type": "Feature", "properties": { "LIB_SITE": "Rohein", "X": -2.630417, "Y": 48.64695, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.630417, 48.64695 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Goue Vas", "X": -2.636567, "Y": 47.253417, "PROGRAMME": "ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -2.636567, 47.253417 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Grand Coin", "X": -3.004233, "Y": 47.407783, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.004233, 47.407783 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Gaouac'h", "X": -4.398067, "Y": 47.807367, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.398067, 47.807367 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pierres Noires", "X": -3.2159, "Y": 47.598067, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.2159, 47.598067 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ile Dumet", "X": -2.623133, "Y": 47.408667, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.623133, 47.408667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Bonen", "X": -2.65305, "Y": 47.303917, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.65305, 47.303917 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Cancavale", "X": -2.018067, "Y": 48.604633, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.018067, 48.604633 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Haie de la Conch‚e", "X": -2.045717, "Y": 48.687067, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.045717, 48.687067 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Vieux Banc", "X": -2.167383, "Y": 48.699133, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.167383, 48.699133 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Kein an duono", "X": -3.145533, "Y": 48.889183, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -3.145533, 48.889183 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Moguedhier", "X": -3.056567, "Y": 48.838983, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.056567, 48.838983 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Paon", "X": -2.984967, "Y": 48.866383, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.984967, 48.866383 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Squ‚ouel", "X": -3.474583, "Y": 48.837417, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.474583, 48.837417 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Roc'h Mignon", "X": -3.5768, "Y": 48.756183, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.5768, 48.756183 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Roc'h Parou", "X": -3.620167, "Y": 48.715667, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.620167, 48.715667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Triagoz", "X": -3.6466, "Y": 48.871267, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -3.6466, 48.871267 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La BarriŠre", "X": -3.51345, "Y": 48.888767, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.51345, 48.888767 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Corbeau", "X": -3.888267, "Y": 48.6769, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.888267, 48.6769 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Penven", "X": -4.005867, "Y": 48.759633, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.005867, 48.759633 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Œles de la croix", "X": -4.603867, "Y": 48.615483, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.603867, 48.615483 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Liniou", "X": -4.8077, "Y": 48.490233, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.8077, 48.490233 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Morvan", "X": -4.585767, "Y": 48.638567, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -4.585767, 48.638567 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Fort de la Fraternit‚", "X": -4.577333, "Y": 48.3096, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.577333, 48.3096 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Gorle Vihan", "X": -5.043467, "Y": 48.47205, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -5.043467, 48.47205 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ile Ronde", "X": -4.4634, "Y": 48.32465, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.4634, 48.32465 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ar Forc'h Vihan", "X": -5.141717, "Y": 48.445367, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -5.141717, 48.445367 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Ile de l'Aber", "X": -4.437717, "Y": 48.221833, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.437717, 48.221833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Van", "X": -4.717133, "Y": 48.066083, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.717133, 48.066083 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Bluiniers", "X": -4.063533, "Y": 47.722467, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.063533, 47.722467 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Linuen", "X": -3.96295, "Y": 47.844217, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.96295, 47.844217 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "les Poulains", "X": -4.056917, "Y": 47.793583, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -4.056917, 47.793583 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pen a Men", "X": -3.951233, "Y": 47.721667, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.951233, 47.721667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Trou d'Enfer", "X": -3.465867, "Y": 47.621317, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.465867, 47.621317 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Bastresse Sud", "X": -3.36735, "Y": 47.681817, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.36735, 47.681817 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Magou‰r Nord", "X": -3.210717, "Y": 47.661117, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.210717, 47.661117 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Tourelle de Gr‚gam", "X": -2.9167, "Y": 47.56565, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.9167, 47.56565 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Pointe du Grand Guet", "X": -3.249933, "Y": 47.316767, "PROGRAMME": "REBENT\/DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.249933, 47.316767 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Er Pondeux", "X": -3.074467, "Y": 47.452117, "PROGRAMME": "REBENT", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -3.074467, 47.452117 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Wissant", "X": 1.676667, "Y": 50.912333, "PROGRAMME": "DCE", "OPERATEUR_": "Station de Wimer", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ 1.676667, 50.912333 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Audresselles", "X": 1.5845, "Y": 50.832833, "PROGRAMME": "DCE", "OPERATEUR_": "Station de Wimer", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ 1.5845, 50.832833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Saint Aubin", "X": -0.42885, "Y": 49.352833, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -0.42885, 49.352833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Tatihou", "X": -1.231933, "Y": 49.585867, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.231933, 49.585867 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Cap Levi", "X": -1.467817, "Y": 49.690883, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.467817, 49.690883 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Cap de Flamanville", "X": -1.894817, "Y": 49.529033, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.894817, 49.529033 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Ecrehou", "X": -1.937067, "Y": 49.2723, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.937067, 49.2723 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Chausey", "X": -1.85205, "Y": 48.865067, "PROGRAMME": "DCE", "OPERATEUR_": "MNHN CC", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.85205, 48.865067 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Guetary Sud", "X": -1.618, "Y": 43.428583, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.618, 43.428583 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Les Jumeaux", "X": -1.756583, "Y": 43.385567, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.756583, 43.385567 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Soccoa", "X": -1.689, "Y": 43.396667, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.689, 43.396667 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Le Pilier", "X": -2.377417, "Y": 47.045083, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.377417, 47.045083 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Yeu Basse Flore", "X": -2.40571, "Y": 46.7322, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.40571, 46.7322 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La Vigie", "X": -2.01735, "Y": 46.721367, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.01735, 46.721367 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Phare des baleines", "X": -1.592167, "Y": 46.2476, "PROGRAMME": "DCE", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -1.592167, 46.2476 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Guetary Nord", "X": -1.60625, "Y": 43.4289, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.60625, 43.4289 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Viviers Basques", "X": -1.712017, "Y": 43.389367, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.712017, 43.389367 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Port Vieux", "X": -1.5717, "Y": 43.483133, "PROGRAMME": "DCE", "OPERATEUR_": "Ifremer Anglet", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.5717, 43.483133 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Dielette", "X": -1.869833, "Y": 49.550517, "PROGRAMME": "DCE", "OPERATEUR_": "Ecosub", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.869833, 49.550517 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Gouville", "X": -1.648583, "Y": 49.107267, "PROGRAMME": "DCE", "OPERATEUR_": "Ecosub", "STATUT_DU_": "inactif" }, "geometry": { "type": "Point", "coordinates": [ -1.648583, 49.107267 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Le Croisic SR", "X": -2.559867, "Y": 47.30305, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.559867, 47.30305 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Penchateau SR", "X": -2.412467, "Y": 47.256833, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.412467, 47.256833 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "Baguenaud SR", "X": -2.35355, "Y": 47.232017, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.35355, 47.232017 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La Banche Nord SR", "X": -2.4672, "Y": 47.184617, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.4672, 47.184617 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La Pointe Saint Gildas", "X": -2.253433, "Y": 47.134083, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.253433, 47.134083 ] } },
+{ "type": "Feature", "properties": { "LIB_SITE": "La Banche Sud SR", "X": -2.467883, "Y": 47.17335, "PROGRAMME": "DCE\/ELV", "OPERATEUR_": "Bio-Littoral", "STATUT_DU_": "actif" }, "geometry": { "type": "Point", "coordinates": [ -2.467883, 47.17335 ] } }
+]
+}
diff -r 642e31c435c9 -r 59349973537f test-data/entities.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/entities.txt	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,4 @@
+objectName	variable	value
+data_7.GeoJSON	geometry	Point
+data_7.GeoJSON	geometricObjectCount	65
+data_7.GeoJSON	spatialReference	GCS_WGS_1984
diff -r 642e31c435c9 -r 59349973537f vector_templates.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vector_templates.R	Sat Dec 23 20:41:10 2023 +0000
@@ -0,0 +1,22 @@
+#15/12/2023 #SEGUINEAU Pauline 
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+    data_vector <- commandArgs(trailingOnly = TRUE)[1]   
+}
+
+#Transform arguments
+
+vector =  strsplit(data_vector," ")
+
+#Make templates to describe data raster
+
+template_vector_attributes(path = ".",data.path= "data_files", vector.file = vector[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+
+