diff annotations_template.xml @ 3:c9a9024c7cb7 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit e519c7f66456a43f9beb69209a3eb45723065216

--- 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?**
 --------------------