Mercurial > repos > ieguinoa > ena_upload
comparison samples_macros.xml @ 2:2f7a70c0d3ab draft default tip
Uploaded
| author | ieguinoa |
|---|---|
| date | Mon, 21 Feb 2022 14:22:53 +0000 |
| parents | 5d59238cd3f4 |
| children |
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| 1:9681a9180730 | 2:2f7a70c0d3ab |
|---|---|
| 65 </conditional> | 65 </conditional> |
| 66 </xml> | 66 </xml> |
| 67 <xml name="table_inputs_macro"> | 67 <xml name="table_inputs_macro"> |
| 68 <conditional name="input_format_conditional"> | 68 <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?"> | 69 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> |
| 70 <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> |
| 71 <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> |
| 72 <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> |
| 73 </param> | 73 </param> |
| 74 <when value="excel_tables"> | 74 <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)" />--> | 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)" />--> |
| 76 <expand macro="checklist_input_macro"/> | 76 <expand macro="checklist_input_macro"/> |
| 77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" /> | 77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" /> |
| 78 <expand macro="run_inputs_macro" /> | 78 <expand macro="run_inputs_macro" /> |
| 79 </when> | 79 </when> |
| 80 <when value="user_generated_tables"> | 80 <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)" />--> | 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"/> | 82 <expand macro="checklist_input_macro"/> |
| 205 <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)"/> |
| 206 <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" > |
| 207 <param name="sample_title" type="text" label="Sample title"/> | 207 <param name="sample_title" type="text" label="Sample title"/> |
| 208 <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"/> |
| 209 <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"/> |
| 210 <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" /> |
| 211 <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" > |
| 212 <param name="experiment_title" type="text" label="Specify an experiment title" /> | 212 <param name="experiment_title" type="text" label="Specify an experiment title" /> |
| 213 <param name="experiment_design" type="text" label="Describe the experiment design" /> | 213 <param name="experiment_design" type="text" label="Describe the experiment design" /> |
| 214 <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"> |
| 215 <options from_data_table="library_strategy"> | 215 <options from_data_table="library_strategy"> |