Mercurial > repos > iuc > ena_upload
diff samples_macros.xml @ 7:6f6537780379 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
author | iuc |
---|---|
date | Thu, 24 Feb 2022 18:20:40 +0000 |
parents | 26ccb678abc8 |
children | 480d9e9d156b |
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--- a/samples_macros.xml Mon Nov 15 11:47:13 2021 +0000 +++ b/samples_macros.xml Thu Feb 24 18:20:40 2022 +0000 @@ -1,4 +1,48 @@ <macros> + <xml name="checklist_input_macro"> + <param type="select" name="checklist_id" label="Select the metadata checklist" help="You can find metadata templates for each checklist at: https://github.com/ELIXIR-Belgium/ENA-metadata-templates"> + <option value="ERC000011">ENA default sample checklist (ERC000011)</option> + <option value="ERC000012">GSC MIxS air (ERC000012)</option> + <option value="ERC000013">GSC MIxS host associated (ERC000013)</option> + <option value="ERC000014">GSC MIxS human associated (ERC000014)</option> + <option value="ERC000015">GSC MIxS human gut (ERC000015)</option> + <option value="ERC000016">GSC MIxS human oral (ERC000016)</option> + <option value="ERC000017">GSC MIxS human skin (ERC000017)</option> + <option value="ERC000018">GSC MIxS human vaginal (ERC000018)</option> + <option value="ERC000019">GSC MIxS microbial mat biolfilm (ERC000019)</option> + <option value="ERC000020">GSC MIxS plant associated (ERC000020)</option> + <option value="ERC000021">GSC MIxS sediment (ERC000021)</option> + <option value="ERC000022">GSC MIxS soil (ERC000022)</option> + <option value="ERC000023">GSC MIxS wastewater sludge (ERC000023)</option> + <option value="ERC000024">GSC MIxS water (ERC000024)</option> + <option value="ERC000025">GSC MIxS miscellaneous natural or artificial environment (ERC000025)</option> + <option value="ERC000027">ENA Micro B3 (ERC000027)</option> + <option value="ERC000028">ENA prokaryotic pathogen minimal sample checklist (ERC000028)</option> + <option value="ERC000029">ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1 (ERC000029)</option> + <option value="ERC000030">ENA Tara Oceans (ERC000030)</option> + <option value="ERC000031">GSC MIxS built environment (ERC000031)</option> + <option value="ERC000032">ENA Influenza virus reporting standard checklist (ERC000032)</option> + <option value="ERC000033">ENA virus pathogen reporting standard checklist (ERC000033)</option> + <option value="ERC000034">ENA mutagenesis by carcinogen treatment checklist (ERC000034)</option> + <option value="ERC000035">ENA Crop Plant sample enhanced annotation checklist (ERC000035)</option> + <option value="ERC000036">ENA sewage checklist (ERC000036)</option> + <option value="ERC000037">ENA Plant Sample Checklist (ERC000037)</option> + <option value="ERC000038">ENA Shellfish Checklist (ERC000038)</option> + <option value="ERC000039">ENA parasite sample checklist (ERC000039)</option> + <option value="ERC000040">ENA UniEuk_EukBank Checklist (ERC000040)</option> + <option value="ERC000041">ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist (ERC000041)</option> + <option value="ERC000043">ENA Marine Microalgae Checklist (ERC000043)</option> + <option value="ERC000044">COMPARE-ECDC-EFSA pilot human-associated reporting standard (ERC000044)</option> + <option value="ERC000045">COMPARE-ECDC-EFSA pilot food-associated reporting standard (ERC000045)</option> + <option value="ERC000047">GSC MIMAGS (ERC000047)</option> + <option value="ERC000048">GSC MISAGS (ERC000048)</option> + <option value="ERC000049">GSC MIUVIGS (ERC000049)</option> + <option value="ERC000050">ENA binned metagenome (ERC000050)</option> + <option value="ERC000051">PDX Checklist (ERC000051)</option> + <option value="ERC000052">HoloFood Checklist (ERC000052)</option> + <option value="ERC000053">Tree of Life Checklist (ERC000053)</option> + </param> + </xml> <xml name="test_submit_section"> <section name="test_submit_parameters" expanded="true" title="Testing options"> <param name="submit_dev" type="boolean" truevalue="true" falsevalue="false" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" /> @@ -23,17 +67,19 @@ <xml name="table_inputs_macro"> <conditional name="input_format_conditional"> <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> - <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option> + <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option> <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> </param> <when value="excel_tables"> - <param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" /> - <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" /> + <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />--> + <expand macro="checklist_input_macro"/> + <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" /> <expand macro="run_inputs_macro" /> </when> <when value="user_generated_tables"> - <param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" /> + <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />--> + <expand macro="checklist_input_macro"/> <expand macro="run_inputs_macro" /> <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> @@ -161,7 +207,7 @@ <param name="sample_title" type="text" label="Sample title"/> <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/> - <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" /> + <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" /> <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > <param name="experiment_title" type="text" label="Specify an experiment title" /> <param name="experiment_design" type="text" label="Describe the experiment design" />