comparison samples_macros.xml @ 11:f803a68fc9e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d

10:480d9e9d156b

<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="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 template</option>
                <option value="build_tables" selected="False">Interactive generation of the study structure (only 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 template" />
                <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"/>

                <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="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.">
                        <option value="True" selected="True">Viral</option>
                        <option value="False" selected="False">Non viral</option>
                    </param>

                    <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"/>

11:f803a68fc9e5

<macros>
    <xml name="checklist_input_macro">
        <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">
            <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="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="Submissions options">
            <param name="center" type="text" optional="False" label="Affiliation center"/>
            <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/." />
            <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."/>
        </section>
    </xml>
    <xml name="run_inputs_macro">
        <conditional name="run_input_format_conditional">
            <param name="run_input_format" type="select" label="Select input data">
                <option value="multiple_selection_list" selected="True">Dataset or dataset collection</option>
                <option value="paired_list" selected="False">Paired dataset 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 dataset or 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 sequencing data 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="Select the metadata input method">
                <option value="excel_tables" selected="True">Excel file</option>
                <option value="user_generated_tables" selected="False">Tabular files (studies - samples - experiments - runs)</option>
                <option value="isa_json" selected="False">ISA json file</option>
                <option value="build_tables" selected="False">Interactively (only recommended for small studies)</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 template" />
                <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"/>

                <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="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.">
                        <option value="True" selected="True">Viral</option>
                        <option value="False" selected="False">Non viral</option>
                    </param>

                    <when value="False">
                        <expand macro="nonviral_samples" />
                    </when>
                </conditional>
            </when>
            <when value="isa_json">
                <param name="isa_json_file" type="data" format="json" label="Select ISA json file" />
                <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)" />
                <expand macro="run_inputs_macro" />
            </when>
        </conditional>
        
    </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"/>