annotate samples_macros.xml @ 9:a62c4a11a67d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379

<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 template</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 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"/>
                <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="integer" value="0" 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>