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comparison samples_macros.xml @ 11:f803a68fc9e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
author iuc
date Sat, 23 Mar 2024 22:06:45 +0000
parents 480d9e9d156b
children 29648e5e83a8
comparison
equal deleted inserted replaced
10:480d9e9d156b 11:f803a68fc9e5
1 <macros> 1 <macros>
2 <xml name="checklist_input_macro"> 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"> 3 <param type="select" name="checklist_id" label="Select the ENA sample 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> 4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option>
5 <option value="ERC000012">GSC MIxS air (ERC000012)</option> 5 <option value="ERC000012">GSC MIxS air (ERC000012)</option>
6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option> 6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option>
7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option> 7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option>
8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option> 8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option>
42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option> 42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option>
43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option> 43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option>
44 </param> 44 </param>
45 </xml> 45 </xml>
46 <xml name="test_submit_section"> 46 <xml name="test_submit_section">
47 <section name="test_submit_parameters" expanded="True" title="Testing options"> 47 <section name="test_submit_parameters" expanded="True" title="Submissions options">
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/" /> 48 <param name="center" type="text" optional="False" label="Affiliation center"/>
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."/> 49 <param name="submit_dev" type="boolean" truevalue="True" falsevalue="False" label="Submit to ENA test server" help="Uploads to the test server of ENA will not be made public and will be removed automatically in 24 hours. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find these uploads at https://wwwdev.ebi.ac.uk/ena/." />
50 <param name="dry_run" type="boolean" truevalue="True" falsevalue="False" label="Create test outputs without submitting (meta)data to ENA" help="If yes is selected then NO submission will be performed."/>
50 </section> 51 </section>
51 </xml> 52 </xml>
52 <xml name="run_inputs_macro"> 53 <xml name="run_inputs_macro">
53 <conditional name="run_input_format_conditional"> 54 <conditional name="run_input_format_conditional">
54 <param name="run_input_format" type="select" label="Select runs input format"> 55 <param name="run_input_format" type="select" label="Select input data">
55 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> 56 <option value="multiple_selection_list" selected="True">Dataset or dataset collection</option>
56 <option value="paired_list" selected="False">Input from a paired collection</option> 57 <option value="paired_list" selected="False">Paired dataset collection</option>
57 </param> 58 </param>
58 <when value="multiple_selection_list"> 59 <when value="multiple_selection_list">
59 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/> 60 <param name="add_extension" type="boolean" checked="False" label="Add .fastq (.gz, .bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
60 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/> 61 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select dataset or dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
61 </when> 62 </when>
62 <when value="paired_list"> 63 <when value="paired_list">
63 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" /> 64 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end sequencing data files" help="Names should match the compressed run's files names defined in the metadata" />
64 </when> 65 </when>
65 </conditional> 66 </conditional>
66 </xml> 67 </xml>
67 <xml name="table_inputs_macro"> 68 <xml name="table_inputs_macro">
68 <conditional name="input_format_conditional"> 69 <conditional name="input_format_conditional">
69 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> 70 <param name="input_format" type="select" label="Select the metadata input method">
70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option> 71 <option value="excel_tables" selected="True">Excel file</option>
71 <option value="build_tables" selected="False">Interactive generation of the study structure (only recommended for small studies)</option> 72 <option value="user_generated_tables" selected="False">Tabular files (studies - samples - experiments - runs)</option>
72 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> 73 <option value="isa_json" selected="False">ISA json file</option>
74 <option value="build_tables" selected="False">Interactively (only recommended for small studies)</option>
73 </param> 75 </param>
74 <when value="excel_tables"> 76 <when value="excel_tables">
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)" />--> 77 <!--<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)" />-->
76 <expand macro="checklist_input_macro"/> 78 <expand macro="checklist_input_macro"/>
77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" /> 79 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (.xlsx) file based on template" />
78 <expand macro="run_inputs_macro" /> 80 <expand macro="run_inputs_macro" />
79 </when> 81 </when>
80 <when value="user_generated_tables"> 82 <when value="user_generated_tables">
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)" />--> 83 <!--<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"/> 84 <expand macro="checklist_input_macro"/>
85 <param name="samples_users_table" type="data" format="tabular" multiple="False" label="Samples table" help="Samples metadata file"/> 87 <param name="samples_users_table" type="data" format="tabular" multiple="False" label="Samples table" help="Samples metadata file"/>
86 <param name="experiments_users_table" type="data" format="tabular" multiple="False" label="Experiments table" help="Experiments metadata file"/> 88 <param name="experiments_users_table" type="data" format="tabular" multiple="False" label="Experiments table" help="Experiments metadata file"/>
87 <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/> 89 <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/>
88 </when> 90 </when>
89 <when value="build_tables"> 91 <when value="build_tables">
90 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/> 92 <param name="add_extension" type="boolean" checked="False" label="Add .fastq (.gz, .bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
91 <conditional name="conditional_viral_metadata"> 93 <conditional name="conditional_viral_metadata">
92 <param name="viral_sample" type="select" label="Select your sample type" help="Non-viral interactive submissions lack specific sample checklist attributes and are suboptimal. It's highly recommended to use Excel or TSV templates as input for a more comprehensive submission."> 94 <param name="viral_sample" type="select" label="Select your sample type" help="Non-viral interactive submissions lack specific sample checklist attributes and are suboptimal. It's highly recommended to use Excel or TSV templates as input for a more comprehensive submission.">
93 <option value="True" selected="True">Viral</option> 95 <option value="True" selected="True">Viral</option>
94 <option value="False" selected="False">Non viral</option> 96 <option value="False" selected="False">Non viral</option>
95 </param> 97 </param>
99 <when value="False"> 101 <when value="False">
100 <expand macro="nonviral_samples" /> 102 <expand macro="nonviral_samples" />
101 </when> 103 </when>
102 </conditional> 104 </conditional>
103 </when> 105 </when>
106 <when value="isa_json">
107 <param name="isa_json_file" type="data" format="json" label="Select ISA json file" />
108 <param name="isa_assay_stream" type="text" optional="False" help="List the assay_stream values from the comment field in the assays list of the ISA-json you want to submit." label="Specify the ISA json assay stream(s)" />
109 <expand macro="run_inputs_macro" />
110 </when>
104 </conditional> 111 </conditional>
105 <param name="center" type="text" optional="False" label="Affiliation center"/> 112
106 </xml> 113 </xml>
107 <xml name="viral_samples"> 114 <xml name="viral_samples">
108 <repeat name="rep_study" title="Study" min="1"> 115 <repeat name="rep_study" title="Study" min="1">
109 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> 116 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
110 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> 117 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>