# HG changeset patch
# User ecology
# Date 1769787551 0
# Node ID c9a9024c7cb7926fb0f0065f1519bdf8265e611d
# Parent  79f2ca0bfa9ab7eb9a3e9ce068fc1552c67d13b7
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit e519c7f66456a43f9beb69209a3eb45723065216

diff -r 79f2ca0bfa9a -r c9a9024c7cb7 annotations_template.xml
--- a/annotations_template.xml	Thu Jan 16 15:56:27 2025 +0000
+++ b/annotations_template.xml	Fri Jan 30 15:39:11 2026 +0000
@@ -1,8 +1,8 @@
-<tool id="annotations_template" name="Make annotations template" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="annotations_template" name="Make annotations template" version="0.1.2+galaxy0" python_template_version="3.5" profile="21.05">
     <description>from scratch or from EML metadata file</description>
     <requirements>
         <requirement type="package" version="4.4.1">r-base</requirement>
-        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
+        <container type="docker">ylebras/metashark:1.7.6</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
    
@@ -120,31 +120,45 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-           <param name="input_prod_selector" value="fr_EML"/>
-           <param name="inputEML" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
-           <output name="output" file="annotemp/annotations_template.txt"/>
+            <conditional name="input_prod">
+                <param name="input_prod_selector" value="fr_EML"/>
+                <param name="inputEML" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
+            </conditional>
+            <output name="output" file="annotemp/annotations_template.txt"/>
         </test>
         <test expect_num_outputs="1">
-           <param name="input_prod_selector" value="fr_scratch"/>
-           <param name="input_selector" value="both"/>
-           <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/>
-           <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
-           <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/> 
-           <output name="output" file="annotemp/annotations_template_2.txt"/>
+            <conditional name="input_prod">
+                <param name="input_prod_selector" value="fr_scratch"/>
+                <conditional name="input">
+                    <param name="input_selector" value="both"/>
+                    <param name="inputdata" value="annotemp/ceamarc_env.tsv"/>
+                    <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
+                    <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
+                </conditional>
+            </conditional>
+            <output name="output" file="annotemp/annotations_template_2.txt"/>
         </test>
         <test expect_num_outputs="1">
-           <param name="input_prod_selector" value="fr_scratch"/>
-           <param name="input_selector" value="data_table"/>
-           <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/>
-           <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/> 
-           <output name="output" file="annotemp/annotations_template_3.txt"/>
+            <conditional name="input_prod">
+                <param name="input_prod_selector" value="fr_scratch"/>
+                <conditional name="input">
+                    <param name="input_selector" value="data_table"/>
+                    <param name="inputdata" value="annotemp/ceamarc_env.tsv"/>
+                    <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
+                </conditional>
+            </conditional>
+            <output name="output" file="annotemp/annotations_template_3.txt"/>
         </test>
         <test expect_num_outputs="1">
-           <param name="input_prod_selector" value="fr_scratch"/>
-           <param name="input_selector" value="other_entities"/>
-           <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
-           <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/> 
-           <output name="output" file="annotemp/annotations_template_4.txt"/>
+            <conditional name="input_prod">
+                <param name="input_prod_selector" value="fr_scratch"/>
+                <conditional name="input">
+                    <param name="input_selector" value="other_entities"/>
+                    <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
+                    <param name="input_temp" value="annotemp/abstract.txt,annotemp/personnel.txt,annotemp/keywords.txt,annotemp/geographic_coverage.txt,annotemp/methods.txt,annotemp/custom_units.txt,annotemp/attributes_ceamarc_env.txt"/>
+                </conditional>
+            </conditional>
+            <output name="output" file="annotemp/annotations_template_4.txt"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -152,7 +166,7 @@
 **What it does?**
 --------------------
 
-This tool is made to produce an annotation template to adds semantic meaning to dataset features (variables, locations, persons, etc.) through links to ontology terms. Template produced can be used in the make EML tool to produce EML metadata Annotating a dataset enables greater human understanding and machine actionability (linked data) and vastly improves the accuracy of future user searches and the interoperability of data in general.
+This tool is made to produce an annotation template to adds semantic meaning to dataset features (variables, locations, persons, etc.) through links to ontology terms. Template produced can be used in the make EML tool to produce EML metadata. Annotating a dataset enables greater human understanding and machine actionability (linked data) and vastly improves the accuracy of future user searches and the interoperability of data in general.
 
 **How to use it?**
 --------------------
diff -r 79f2ca0bfa9a -r c9a9024c7cb7 test-data/taxonomic_coverage.txt
--- a/test-data/taxonomic_coverage.txt	Thu Jan 16 15:56:27 2025 +0000
+++ b/test-data/taxonomic_coverage.txt	Fri Jan 30 15:39:11 2026 +0000
@@ -1,5 +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	NA	NA	NA
-Ammothea_adunca	scientific	Ammothea adunca	GBIF Backbone Taxonomy	5720487
+Achelia_sp	scientific	Achelia	Global Biodiversity Information Facility Backbone Taxonomy	2118396
+Achelia_spicata	scientific	Achelia spicata	Global Biodiversity Information Facility Backbone Taxonomy	4338694
+Achelia_suflata	scientific	Achelia suflata	Global Biodiversity Information Facility Backbone Taxonomy	NA
+Ammothea_adunca	scientific	Ammothea adunca	Global Biodiversity Information Facility Backbone Taxonomy	5720487