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comparison annotations_template.xml @ 3:c9a9024c7cb7 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit e519c7f66456a43f9beb69209a3eb45723065216
author ecology
date Fri, 30 Jan 2026 15:39:11 +0000
parents fab3ca90cb26
children
comparison
equal deleted inserted replaced
2:79f2ca0bfa9a 3:c9a9024c7cb7
1 <tool id="annotations_template" name="Make annotations template" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> 1 <tool id="annotations_template" name="Make annotations template" version="0.1.2+galaxy0" python_template_version="3.5" profile="21.05">
2 <description>from scratch or from EML metadata file</description> 2 <description>from scratch or from EML metadata file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.4.1">r-base</requirement> 4 <requirement type="package" version="4.4.1">r-base</requirement>
5 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container> 5 <container type="docker">ylebras/metashark:1.7.6</container>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 8
9 #if str($input_prod.input_prod_selector) == "fr_EML" 9 #if str($input_prod.input_prod_selector) == "fr_EML"
10 mkdir data_files && 10 mkdir data_files &&
118 <outputs> 118 <outputs>
119 <data name="output" from_work_dir="data_files/annotations.txt" format="txt" label="annotations.txt"/> 119 <data name="output" from_work_dir="data_files/annotations.txt" format="txt" label="annotations.txt"/>
120 </outputs> 120 </outputs>
121 <tests> 121 <tests>
122 <test expect_num_outputs="1"> 122 <test expect_num_outputs="1">
123 <param name="input_prod_selector" value="fr_EML"/> 123 <conditional name="input_prod">
124 <param name="inputEML" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/> 124 <param name="input_prod_selector" value="fr_EML"/>
125 <output name="output" file="annotemp/annotations_template.txt"/> 125 <param name="inputEML" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
126 </conditional>
127 <output name="output" file="annotemp/annotations_template.txt"/>
126 </test> 128 </test>
127 <test expect_num_outputs="1"> 129 <test expect_num_outputs="1">
128 <param name="input_prod_selector" value="fr_scratch"/> 130 <conditional name="input_prod">
129 <param name="input_selector" value="both"/> 131 <param name="input_prod_selector" value="fr_scratch"/>
130 <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/> 132 <conditional name="input">
131 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/> 133 <param name="input_selector" value="both"/>
132 <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"/> 134 <param name="inputdata" value="annotemp/ceamarc_env.tsv"/>
133 <output name="output" file="annotemp/annotations_template_2.txt"/> 135 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
136 <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"/>
137 </conditional>
138 </conditional>
139 <output name="output" file="annotemp/annotations_template_2.txt"/>
134 </test> 140 </test>
135 <test expect_num_outputs="1"> 141 <test expect_num_outputs="1">
136 <param name="input_prod_selector" value="fr_scratch"/> 142 <conditional name="input_prod">
137 <param name="input_selector" value="data_table"/> 143 <param name="input_prod_selector" value="fr_scratch"/>
138 <param name="inputdata" value = "annotemp/ceamarc_env.tsv"/> 144 <conditional name="input">
139 <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"/> 145 <param name="input_selector" value="data_table"/>
140 <output name="output" file="annotemp/annotations_template_3.txt"/> 146 <param name="inputdata" value="annotemp/ceamarc_env.tsv"/>
147 <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"/>
148 </conditional>
149 </conditional>
150 <output name="output" file="annotemp/annotations_template_3.txt"/>
141 </test> 151 </test>
142 <test expect_num_outputs="1"> 152 <test expect_num_outputs="1">
143 <param name="input_prod_selector" value="fr_scratch"/> 153 <conditional name="input_prod">
144 <param name="input_selector" value="other_entities"/> 154 <param name="input_prod_selector" value="fr_scratch"/>
145 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/> 155 <conditional name="input">
146 <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"/> 156 <param name="input_selector" value="other_entities"/>
147 <output name="output" file="annotemp/annotations_template_4.txt"/> 157 <param name="input_other" value="annotemp/pivot_wider_jupytool_notebook.ipynb"/>
158 <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"/>
159 </conditional>
160 </conditional>
161 <output name="output" file="annotemp/annotations_template_4.txt"/>
148 </test> 162 </test>
149 </tests> 163 </tests>
150 <help><![CDATA[ 164 <help><![CDATA[
151 165
152 **What it does?** 166 **What it does?**
153 -------------------- 167 --------------------
154 168
155 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. 169 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.
156 170
157 **How to use it?** 171 **How to use it?**
158 -------------------- 172 --------------------
159 173
160 You can run this tool after all your EAL metadata templates are complete or if you're annotating an existing EML file. 174 You can run this tool after all your EAL metadata templates are complete or if you're annotating an existing EML file.