Mercurial > repos > ieguinoa > ena_upload
diff samples_macros.xml @ 0:5d59238cd3f4 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Wed, 02 Feb 2022 17:16:15 +0000 |
| parents | |
| children | 2f7a70c0d3ab |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samples_macros.xml Wed Feb 02 17:16:15 2022 +0000 @@ -0,0 +1,261 @@ +<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/" /> + <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."/> + </section> + </xml> + <xml name="run_inputs_macro"> + <conditional name="run_input_format_conditional"> + <param name="run_input_format" type="select" label="Select runs input format"> + <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> + <option value="paired_list" selected="False">Input from a paired collection</option> + </param> + <when value="multiple_selection_list"> + <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?"/> + <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"/> + </when> + <when value="paired_list"> + <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" /> + </when> + </conditional> + </xml> + <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="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)" />--> + <expand macro="checklist_input_macro"/> + <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" /> + <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)" />--> + <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"/> + <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> + <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> + </when> + <when value="build_tables"> + <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?"/> + <conditional name="conditional_viral_metadata"> + <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" /> + <when value="true"> + <expand macro="viral_samples" /> + </when> + <when value="false"> + <expand macro="nonviral_samples" /> + </when> + </conditional> + </when> + </conditional> + <param name="center" type="text" optional="False" label="Affiliation center"/> + </xml> + <xml name="viral_samples"> + <repeat name="rep_study" title="Study" min="1"> + <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> + <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> + <param name="study_type" type="select" label="Please select the type of study"> + <options from_data_table="study_type"> + <column name="value" index="0"/> + </options> + </param> + <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> + <repeat name="rep_sample" title="Samples associated with this study" min="1" > + <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="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided"> + <option value="not collected">not collected</option> + <option value="restricted access">restricted access</option> + <option value="not provided">not provided</option> + <validator type="regex" message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)</validator> + </param> + <param name="geo_location_country" type="select" label="Select the country where the sample was obtained"> + <options from_data_table="geographic_location_1"> + <column name="value" index="0"/> + </options> + </param> + <param name="host_common_name" type="text" label="Host common name" help="e.g human"/> + <param name="host_subject_id" type="text" label="Host subject id"/> + <param name="host_health_state" type="select" label="Host health state"> + <options from_data_table="host_health_state_1"> + <column name="value" index="0"/> + </options> + </param> + <param name="host_sex" type="select" label="Host sex"> + <options from_data_table="host_sex_1"> + <column name="value" index="0"/> + </options> + </param> + <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/> + <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/> + <param name="collecting_institution" type="text" label="Collecting institution"/> + <param name="isolate" type="text" label="Isolate"/> + <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" /> + <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library"> + <options from_data_table="library_strategy"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced"> + <options from_data_table="library_source"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced"> + <options from_data_table="library_selection"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_layout" type="select" label="Library layout"> + <options from_data_table="library_layout"> + <column name="value" index="0"/> + </options> + </param> + <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> + <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> + <param name="platform" type="select" label="Select the sequencing platform used"> + <option value="LS454">LS454</option> + <option value="ILLUMINA">Illumina</option> + <option value="HELICOS">Helicos</option> + <option value="ABI_SOLID">ABI Solid</option> + <option value="COMPLETE_GENOMICS">Complete Genomics</option> + <option value="BGISEQ">BGI Seq</option> + <option value="OXFORD_NANOPORE">Oxford Nanopore</option> + <option value="PACBIO_SMRT">PacBio</option> + <option value="ION_TORRENT">Ion Torrent</option> + <option value="CAPILLARY">Capillary sequencing</option> + </param> + <param name="instrument_model" type="select" label="Instrument model"> + <options from_data_table="instrument_model"> + <column name="value" index="0"/> + </options> + </param> + <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > + <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> + <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> + </repeat> + </repeat> + </repeat> + </repeat> + </xml> + <xml name="nonviral_samples"> + <repeat name="rep_study" title="Study" min="1"> + <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> + <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> + <param name="study_type" type="select" label="Please select the type of study"> + <options from_data_table="study_type"> + <column name="value" index="0"/> + </options> + </param> + <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> + <repeat name="rep_sample" title="Samples associated with this study" min="1" > + <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" /> + <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" /> + <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library"> + <options from_data_table="library_strategy"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced"> + <options from_data_table="library_source"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced"> + <options from_data_table="library_selection"> + <column name="value" index="0"/> + </options> + </param> + <param name="library_layout" type="select" label="Library layout"> + <options from_data_table="library_layout"> + <column name="value" index="0"/> + </options> + </param> + <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> + <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> + <param name="platform" type="select" label="Select the sequencing platform used"> + <option value="LS454">LS454</option> + <option value="ILLUMINA" selected="True">Illumina</option> + <option value="HELICOS">Helicos</option> + <option value="ABI_SOLID">ABI Solid</option> + <option value="COMPLETE_GENOMICS">Complete Genomics</option> + <option value="BGISEQ">BGI Seq</option> + <option value="OXFORD_NANOPORE">Oxford Nanopore</option> + <option value="PACBIO_SMRT">PacBio</option> + <option value="ION_TORRENT">Ion Torrent</option> + <option value="CAPILLARY">Capillary sequencing</option> + </param> + <param name="instrument_model" type="select" label="Instrument model"> + <options from_data_table="instrument_model"> + <column name="value" index="0"/> + </options> + </param> + <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > + <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> + <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> + </repeat> + </repeat> + </repeat> + </repeat> + </xml> +</macros>