# HG changeset patch
# User ecology
# Date 1701481800 0
# Node ID 8a697f446051825052879b59345ef9303ac2e527
# Parent  9d56f64801947cd08ed0e52bf96f867b1aa0eb1a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099

diff -r 9d56f6480194 -r 8a697f446051 geo_cov_temp.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/geo_cov_temp.R	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,37 @@
+#27/11/2023
+#Seguineau Pauline
+#Make geographic coverage template
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  
+  data_table <- args[1]
+  tablename <- args[2]
+  lat_col <- as.numeric(args[3])
+  long_col <- as.numeric(args[4])
+  site_col <- as.numeric(args[5])
+  empty <- args[6]
+}
+
+datatable = read.table(data_table,header=T)
+
+latcol = names(datatable[lat_col])
+longcol = names(datatable[long_col])
+sitecol = names(datatable[site_col])
+
+if (empty == "false"){
+   empty = FALSE
+}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 9d56f6480194 -r 8a697f446051 make_eml.xml
--- a/make_eml.xml	Fri Nov 17 17:07:36 2023 +0000
+++ b/make_eml.xml	Sat Dec 02 01:50:00 2023 +0000
@@ -1,134 +1,134 @@
-<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0">
-    <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>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-    
-    mkdir output_template &&
-    #for $input in $templates
-        ln -s '$input' 'output_template/${input.element_identifier}';
-    #end for
-   
-    #set $table = ""
-    mkdir data_files && 
-    #for $indata in $inputdata
-        ln -s '$indata' 'data_files/${indata.element_identifier}';
-        #set $table += $indata.element_identifier + " ";
-    #end for
-    
-    #set $other = ""
-    #for $data_other in $dataother
-        ln -s '$data_other' 'data_files/${data_other.element_identifier}';
-        #set $other += $data_other.element_identifier + " ";
-    #end for
-  
-    #set $quotetable ="" 
-    #for $q in $table_quote 
-       #set $quotetable += $q.quote + ",";
-    #end for 
-
-    Rscript 
-     '$__tool_directory__/make_eml.R' 2> err.txt
-     '$title'
-     '$temporal_coverage.start'
-     '$temporal_coverage.end'
-     '$table'
-     '$other'
-     '$destable'
-     '$desother'
-     '$quotetable'
-     '$table_url'
-     '$other_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." />
-      <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"/>
-        <repeat name="table_quote" title="What's the quotes of your data table ? Repeat this parameter as many time as the number of data tables you've input and in the same order" >
-                <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true">
-                 <option value="quote">Quote</option>
-                 <option value="apostrophe">Apostrophe</option>
-                 <option value="none">None</option>
-                </param>
-        </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_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="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"/>
-		 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
-    </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>
-            <output name="metadataout" >
-			<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?**
---------------------
-
-This tool produce EML metadata from EAL templates.
-This tool can be used in the continuation of the eml2eal tool.
-
-**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 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>
+<tool id="makeeml" name="Make EML" version="0.1.0+galaxy0" 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>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    
+    mkdir output_template &&
+    #for $input in $templates
+        ln -s '$input' 'output_template/${input.element_identifier}';
+    #end for
+   
+    #set $table = ""
+    mkdir data_files && 
+    #for $indata in $inputdata
+        ln -s '$indata' 'data_files/${indata.element_identifier}';
+        #set $table += $indata.element_identifier + " ";
+    #end for
+    
+    #set $other = ""
+    #for $data_other in $dataother
+        ln -s '$data_other' 'data_files/${data_other.element_identifier}';
+        #set $other += $data_other.element_identifier + " ";
+    #end for
+  
+    #set $quotetable ="" 
+    #for $q in $table_quote 
+       #set $quotetable += $q.quote + ",";
+    #end for 
+
+    Rscript 
+     '$__tool_directory__/make_eml.R' 2> err.txt
+     '$title'
+     '$temporal_coverage.start'
+     '$temporal_coverage.end'
+     '$table'
+     '$other'
+     '$destable'
+     '$desother'
+     '$quotetable'
+     '$table_url'
+     '$other_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." />
+      <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"/>
+        <repeat name="table_quote" title="What's the quotes of your data table ? Repeat this parameter as many time as the number of data tables you've input and in the same order" >
+                <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true">
+                 <option value="quote">Quote</option>
+                 <option value="apostrophe">Apostrophe</option>
+                 <option value="none">None</option>
+                </param>
+        </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_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="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"/>
+		 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
+    </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>
+            <output name="metadataout" >
+			<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?**
+--------------------
+
+This tool produce EML metadata from EAL templates.
+This tool can be used in the continuation of the eml2eal tool.
+
+**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 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 9d56f6480194 -r 8a697f446051 table_templates.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/table_templates.R	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,21 @@
+#28/11/2023 #SEGUINEAU Pauline 
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+if (length(commandArgs(trailingOnly = TRUE)) > 0) {
+    data_table <- commandArgs(trailingOnly = TRUE)[1]
+}
+
+#Transform arguments
+
+table =  strsplit(data_table," ")
+
+#Make templates to describe data tables : Describes columns of a data table (classes, units, datetime formats, missing value codes) + catégorical variables.
+
+template_table_attributes(path = ".",data.path= "data_files", data.table = table[[1]])
+template_categorical_variables(path = ".", data.path = "data_files")
+
diff -r 9d56f6480194 -r 8a697f446051 taxo_cov_template.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxo_cov_template.R	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,47 @@
+#28/11/2023
+#Seguineau Pauline
+#Make taxonomic coverage template
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  data_taxa <- args[1]
+  taxa_table <- args[2]
+  taxa_col <- as.numeric(args[3])
+  taxa_name_type <- args[4]
+  authority <- as.numeric(args[5])
+  authority2 <- as.numeric(args[6])
+  authority3 <- as.numeric(args[7])
+  empty <- args[8]
+}
+
+#transfom arguments
+taxatable = read.table(data_taxa,header=T,sep="\t")
+taxacol = names(taxatable[taxa_col])
+
+if (authority2 == 0 && authority3==0){
+   authority_f = authority}
+   
+if(authority2 == 0 && authority3 != 0){
+   authority_f = c(authority,authority3)}
+
+if (authority2 !=0 && authority3==0){
+   authority_f = c(authority,authority2)}
+
+if (authority3 !=0 && authority2 !=0){
+   authority_f = c(authority,authority2,authority3)}
+   
+if (empty == "false"){
+   empty = FALSE
+}else if (empty=="true"){
+   empty=TRUE}
+
+
+#Make template
+
+template_taxonomic_coverage(path =".", data.path = "data_files", taxa.table = taxa_table, taxa.col = taxacol, taxa.name.type = taxa_name_type , taxa.authority = authority_f, empty = empty)
diff -r 9d56f6480194 -r 8a697f446051 templates1.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates1.R	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,23 @@
+#22/11/2023 #SEGUINEAU Pauline 
+
+###First tool of EML Workflow
+
+#Load packages
+
+library(EMLassemblyline)
+
+#Load arguments
+
+args = commandArgs(trailingOnly=TRUE)
+if(length(args)>0){
+  
+  license <- args[1]
+  file_type <- args[2]
+}
+
+#Make templates to describe core features of a data package (abstract, methods, keywords, personnel, license). 
+
+template_core_metadata(path=".",license = license, file.type = file_type)
+
+
+
diff -r 9d56f6480194 -r 8a697f446051 test-data/datafile_1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datafile_1.tsv	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,113 @@
+Id	density_boats	distance_coast	percentage_turbidity	nb_individual	recorder	min_t	max_wind
+ID1	0	7.083851986	1	1	13740	9	13
+ID2	0	5.057419245	1	1	3760	11.7	15
+ID3	0	14.81271925	1	1	17598	9	13
+ID4	23.38130966	17.39474876	0	1	17607	12.8	24
+ID5	0	13.8788222	1	1	17608	14.3	17
+ID6	0	20.55593297	1	1	13733	20	17
+ID7	0	5.228906117	1	1	10250	14.3	30
+ID8	0	8.18336163	0.963336783	2	13740	11.7	15
+ID9	0	14.77478497	1	1	13733	11.7	15
+ID10	0	18.23789045	1	1	17573	9	13
+ID11	0	30.97770737	0.934057759	2	17608	8.1	13
+ID12	0	14.72135785	0	2	13733	8.1	13
+ID13	0	26.97792869	1	1	17578	8.1	13
+ID14	0	8.63834361	1	1	17329	11.7	15
+ID15	23.42372625	2.371250707	0.611485317	2	17232	14.3	30
+ID16	0	2.058590657	1	1	NA	11.7	15
+ID17	0	14.5557442	1	1	11693	14.3	17
+ID18	0	15.31628381	0.484376584	2	10250	14.2	9
+ID19	22.68310089	18.12266606	1	1	13733	16.9	13
+ID20	0	10.71630644	0.946424061	2	17608	NA	NA
+ID21	0	7.492501839	1	1	17608	14.3	30
+ID22	0	2.455167732	1	1	17578	8.1	13
+ID23	0	0.215005092	0.619357094	2	17608	13.3	0
+ID24	0	20.5942275	0.530977409	2	17573	12.8	24
+ID25	0	0.00565931	1	1	10250	9	13
+ID26	0	4.61669024	1	1	3760	8.1	13
+ID27	0	0.650746944	1	1	13289	NA	NA
+ID28	11.55094443	4.256523462	0.534748923	2	17608	17.4	15
+ID29	25.29249263	0.333785924	0	3	11693	16.9	13
+ID30	5.659985665	3.927116342	1	1	17578	16.9	13
+ID31	0	0.011314137	0	2	13740	20	17
+ID32	0	6.724401426	0.262229612	3	17578	8.5	7
+ID33	0	10.20546782	0.456408314	2	13676	17.8	13
+ID34	0	0.005662514	1	1	13289	9	13
+ID35	0	12.50424544	1	1	13733	13.3	0
+ID36	41.24173899	0.028288543	0	2	17607	NA	NA
+ID37	0	0.707453733	0	2	13733	17.8	13
+ID38	7.278017273	8.411585021	0.521433594	2	17601	17.4	15
+ID39	26.46665163	3.174693	1	1	17598	11.7	15
+ID40	21.65723654	8.846001472	0.672489759	2	17232	9	13
+ID41	0	7.296088753	0.033790965	2	17601	9	13
+ID42	0	0.848848396	0	3	17608	17.4	14
+ID43	0	17.47693701	1	1	NA	8.1	13
+ID44	0	8.040770102	1	1	17329	8.1	13
+ID45	0	9.227200724	1	1	17607	8.1	13
+ID46	0	4.089829166	0	1	17607	17.4	15
+ID47	16.24258106	12.9081546	0.519677866	2	17232	14.3	17
+ID48	0	28.17682685	0	3	13733	14.2	9
+ID49	0	11.13752122	0.568145458	2	17329	12.8	24
+ID50	0	12.15482119	0.744442086	2	13676	17.4	14
+ID51	0	1.075147125	0.126547756	2	17329	17.8	13
+ID52	0	0.639429606	0.318501019	3	17573	17.8	13
+ID53	0	11.34563151	1	1	13289	9	13
+ID54	0	6.070721358	1	1	11693	8.1	13
+ID55	0	2.534940304	1	1	3760	NA	NA
+ID56	0	0	1	1	17608	14.9	13
+ID57	23.6734518	9.73526417	1	1	13733	14.9	13
+ID58	22.77461434	2.30834512	0	2	3760	17.4	15
+ID59	0	9.034849513	1	1	NA	14.3	30
+ID60	0	1.61299451	1	1	17598	8.1	13
+ID61	0	1.550212164	1	1	17601	8.1	13
+ID62	16.6417688	0.198064626	1	1	13676	13.3	0
+ID63	0	0.147167035	0.503759276	2	13740	14.9	13
+ID64	0	1.126075147	1	1	17329	14.2	9
+ID65	0	1.166213768	0.486555056	2	10250	17.4	14
+ID66	0	37.17890687	0.241246715	3	11693	12.3	11
+ID67	0	1.01318843	1	1	NA	11.7	15
+ID68	0	14.97426034	0.513275979	3	17578	8.5	7
+ID69	0	0.050933786	1	1	10250	13.3	0
+ID70	0	1.60733488	1	1	11693	13.3	0
+ID71	0	0.15274085	0.616607437	2	11693	14.9	13
+ID72	0	4.745186863	0.427826338	3	17578	14.9	13
+ID73	0	0.005658029	1	1	13289	17.4	15
+ID74	20.10097018	1.120479882	1	1	17329	9	13
+ID75	0	1.833512535	1	1	11693	9	13
+ID76	0	1.964892412	1	1	3760	14.9	13
+ID77	0	1.024508972	1	1	17598	13.3	0
+ID78	13.02008677	2.446206116	0	2	17601	17.8	13
+ID79	0	5.849408836	0.506514891	2	17601	12.3	11
+ID80	0	0.82602546	1	1	17607	20	17
+ID81	0	6.632335465	1	1	13733	17.8	13
+ID82	9.774097667	2.083923212	0.147137616	2	17329	17.4	14
+ID83	0	0.843046283	1	1	17598	11.7	15
+ID84	0	17.16743054	1	1	3760	9	13
+ID85	0	2.347816248	1	1	17607	13.3	0
+ID86	0	2.089467724	1	1	17608	8.1	13
+ID87	14.70497236	1.782279054	1	1	17329	8.1	13
+ID88	0	1.828267391	1	1	10250	8.1	13
+ID89	19.54258479	2.829334541	1	1	3760	14.3	30
+ID90	22.89867383	0.50376408	1	1	17573	14.3	30
+ID91	0	7.486419194	1	1	13676	14.2	9
+ID92	0	4.612337295	1	1	17601	11.7	15
+ID93	0	20.34521788	1	1	17232	11.7	15
+ID94	0	13.69731259	0.558754442	2	13289	14.3	17
+ID95	0	0.481041313	0.601822162	2	17607	14.3	17
+ID96	0	19.55721647	0.856473518	3	17232	16.9	13
+ID97	0	9.467489106	1	1	10250	17.4	15
+ID98	0	22.78746039	0.460271388	3	11693	14.3	30
+ID99	0	8.380520951	0.769578171	2	17607	9	13
+ID100	32.43763517	0.486507892	0.297384797	4	17573	12.3	11
+ID101	39.87341993	18.47598574	0.377696294	3	17329	NA	NA
+ID102	0	1.482655198	0.420523151	2	17598	NA	NA
+ID103	0	1.188455008	1	1	13289	8.1	13
+ID104	0	2.981949867	1	1	17232	13.3	0
+ID105	6.048310547	0.06224536	1	1	17578	17.4	14
+ID106	0	0.067957866	1	1	17232	17.4	14
+ID107	0	0.305516266	0	1	17598	17.4	14
+ID108	0	1.375212224	0.512278187	2	17601	20	17
+ID109	23.18323585	0.045282164	0.355925541	2	13676	17.4	14
+ID110	0	0	0.599181014	2	17232	13.3	0
+ID111	0	0.050922259	1	1	17329	14.9	13
+ID112	0	0.763920326	1	1	13740	13.3	0
diff -r 9d56f6480194 -r 8a697f446051 test-data/geographic_coverage.txt
--- a/test-data/geographic_coverage.txt	Fri Nov 17 17:07:36 2023 +0000
+++ b/test-data/geographic_coverage.txt	Sat Dec 02 01:50:00 2023 +0000
@@ -1,2 +1,5 @@
 geographicDescription	northBoundingCoordinate	southBoundingCoordinate	eastBoundingCoordinate	westBoundingCoordinate
-Yvelines - Essonne - Seine et Marne	49.08428	48.12266	3.56409	1.60296
+1	-65.999946	-65.999946	142.3360535	142.3360535
+2	-66.394359	-66.394359	140.4840125	140.4840125
+3	-66.023545	-66.023545	142.745584	142.745584
+4	-66.3379125	-66.3379125	144.011634	144.011634
diff -r 9d56f6480194 -r 8a697f446051 test-data/taxa.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxa.tsv	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,5 @@
+taxa	site
+Achelia_sp	1
+Achelia_spicata	2
+Achelia_suflata	2
+Ammothea_adunca	3
diff -r 9d56f6480194 -r 8a697f446051 test-data/taxonomic_coverage.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomic_coverage.txt	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,5 @@
+name	name_type	name_resolved	authority_system	authority_id
+Achelia_sp	scientific	Achelia	GBIF Backbone Taxonomy	2118396
+Achelia_spicata	scientific	Achelia spicata	GBIF Backbone Taxonomy	4338694
+Achelia_suflata	scientific	Achelia suflata	GBIF Backbone Taxonomy	NA
+Ammothea_adunca	scientific	Ammothea adunca	GBIF Backbone Taxonomy	5720487
diff -r 9d56f6480194 -r 8a697f446051 test-data/test-geocov.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-geocov.tabular	Sat Dec 02 01:50:00 2023 +0000
@@ -0,0 +1,5 @@
+site	lat	long
+1	-65.999946	142.3360535
+2	-66.394359	140.4840125
+3	-66.023545	142.745584
+4	-66.3379125	144.011634