Mercurial > repos > iuc > ena_upload

comparison samples_macros.xml @ 7:ae2d35b56645 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
author iuc
date Thu, 24 Feb 2022 18:20:02 +0000
parents 863a964fd1d6
children e7995727674f
comparison
equal deleted inserted replaced
6:1c79c7ee82c4 7:ae2d35b56645
1 <macros> 1 <macros>
2 <xml name="checklist_input_macro">
3 <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">
4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option>
5 <option value="ERC000012">GSC MIxS air (ERC000012)</option>
6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option>
7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option>
8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option>
9 <option value="ERC000016">GSC MIxS human oral (ERC000016)</option>
10 <option value="ERC000017">GSC MIxS human skin (ERC000017)</option>
11 <option value="ERC000018">GSC MIxS human vaginal (ERC000018)</option>
12 <option value="ERC000019">GSC MIxS microbial mat biolfilm (ERC000019)</option>
13 <option value="ERC000020">GSC MIxS plant associated (ERC000020)</option>
14 <option value="ERC000021">GSC MIxS sediment (ERC000021)</option>
15 <option value="ERC000022">GSC MIxS soil (ERC000022)</option>
16 <option value="ERC000023">GSC MIxS wastewater sludge (ERC000023)</option>
17 <option value="ERC000024">GSC MIxS water (ERC000024)</option>
18 <option value="ERC000025">GSC MIxS miscellaneous natural or artificial environment (ERC000025)</option>
19 <option value="ERC000027">ENA Micro B3 (ERC000027)</option>
20 <option value="ERC000028">ENA prokaryotic pathogen minimal sample checklist (ERC000028)</option>
21 <option value="ERC000029">ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1 (ERC000029)</option>
22 <option value="ERC000030">ENA Tara Oceans (ERC000030)</option>
23 <option value="ERC000031">GSC MIxS built environment (ERC000031)</option>
24 <option value="ERC000032">ENA Influenza virus reporting standard checklist (ERC000032)</option>
25 <option value="ERC000033">ENA virus pathogen reporting standard checklist (ERC000033)</option>
26 <option value="ERC000034">ENA mutagenesis by carcinogen treatment checklist (ERC000034)</option>
27 <option value="ERC000035">ENA Crop Plant sample enhanced annotation checklist (ERC000035)</option>
28 <option value="ERC000036">ENA sewage checklist (ERC000036)</option>
29 <option value="ERC000037">ENA Plant Sample Checklist (ERC000037)</option>
30 <option value="ERC000038">ENA Shellfish Checklist (ERC000038)</option>
31 <option value="ERC000039">ENA parasite sample checklist (ERC000039)</option>
32 <option value="ERC000040">ENA UniEuk_EukBank Checklist (ERC000040)</option>
33 <option value="ERC000041">ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist (ERC000041)</option>
34 <option value="ERC000043">ENA Marine Microalgae Checklist (ERC000043)</option>
35 <option value="ERC000044">COMPARE-ECDC-EFSA pilot human-associated reporting standard (ERC000044)</option>
36 <option value="ERC000045">COMPARE-ECDC-EFSA pilot food-associated reporting standard (ERC000045)</option>
37 <option value="ERC000047">GSC MIMAGS (ERC000047)</option>
38 <option value="ERC000048">GSC MISAGS (ERC000048)</option>
39 <option value="ERC000049">GSC MIUVIGS (ERC000049)</option>
40 <option value="ERC000050">ENA binned metagenome (ERC000050)</option>
41 <option value="ERC000051">PDX Checklist (ERC000051)</option>
42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option>
43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option>
44 </param>
45 </xml>
2 <xml name="test_submit_section"> 46 <xml name="test_submit_section">
3 <section name="test_submit_parameters" expanded="true" title="Testing options"> 47 <section name="test_submit_parameters" expanded="true" title="Testing options">
4 <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/" /> 48 <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/" />
5 <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/> 49 <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
6 </section> 50 </section>
21 </conditional> 65 </conditional>
22 </xml> 66 </xml>
23 <xml name="table_inputs_macro"> 67 <xml name="table_inputs_macro">
24 <conditional name="input_format_conditional"> 68 <conditional name="input_format_conditional">
25 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> 69 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
26 <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option> 70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option>
27 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> 71 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
28 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> 72 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
29 </param> 73 </param>
30 <when value="excel_tables"> 74 <when value="excel_tables">
31 <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)" /> 75 <!--<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)" />-->
32 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" /> 76 <expand macro="checklist_input_macro"/>
77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" />
33 <expand macro="run_inputs_macro" /> 78 <expand macro="run_inputs_macro" />
34 </when> 79 </when>
35 <when value="user_generated_tables"> 80 <when value="user_generated_tables">
36 <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)" /> 81 <!--<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)" />-->
82 <expand macro="checklist_input_macro"/>
37 <expand macro="run_inputs_macro" /> 83 <expand macro="run_inputs_macro" />
38 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> 84 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/>
39 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> 85 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
40 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> 86 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
41 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> 87 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
159 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> 205 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
160 <repeat name="rep_sample" title="Samples associated with this study" min="1" > 206 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
161 <param name="sample_title" type="text" label="Sample title"/> 207 <param name="sample_title" type="text" label="Sample title"/>
162 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> 208 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
163 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/> 209 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
164 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" /> 210 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
165 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > 211 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
166 <param name="experiment_title" type="text" label="Specify an experiment title" /> 212 <param name="experiment_title" type="text" label="Specify an experiment title" />
167 <param name="experiment_design" type="text" label="Describe the experiment design" /> 213 <param name="experiment_design" type="text" label="Describe the experiment design" />
168 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library"> 214 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
169 <options from_data_table="library_strategy"> 215 <options from_data_table="library_strategy">