Mercurial > repos > iuc > ena_upload
diff samples_macros.xml @ 1:57251c760cab draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
author | iuc |
---|---|
date | Fri, 30 Apr 2021 12:09:25 +0000 |
parents | 382518f24d6d |
children | 9e2df763086c |
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--- a/samples_macros.xml Sat Nov 28 09:45:44 2020 +0000 +++ b/samples_macros.xml Fri Apr 30 12:09:25 2021 +0000 @@ -1,5 +1,24 @@ <macros> - + <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="data" type="data" format="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="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?"> @@ -9,22 +28,20 @@ </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="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/> - <param name="xlsx_file" type="data" format="xlsx" /> - <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/> + <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)" /> - <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/> + <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="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/> <conditional name="conditional_viral_metadata"> - <param name="viral_sample" type="boolean" label="Does your submission contains viral samples?" /> + <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> @@ -51,8 +68,11 @@ <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 leave blank"> - <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})?)?)?)?)?$)|(^not colected$)|(^not provided$)|(^restricted access$)</validator> + <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"> @@ -118,6 +138,7 @@ </options> </param> <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > + <param name="run_base_name" type="text" optional="False" default="" 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="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> </repeat> </repeat> @@ -166,7 +187,7 @@ <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="ILLUMINA" selected="True">Illumina</option> <option value="HELICOS">Helicos</option> <option value="ABI_SOLID">ABI Solid</option> <option value="COMPLETE_GENOMICS">Complete Genomics</option> @@ -182,6 +203,7 @@ </options> </param> <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > + <param name="run_base_name" type="text" optional="False" default="" 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="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> </repeat> </repeat>