Mercurial > repos > iuc > ena_upload
diff samples_macros.xml @ 0:382518f24d6d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
| author | iuc |
|---|---|
| date | Sat, 28 Nov 2020 09:45:44 +0000 |
| parents | |
| children | 57251c760cab |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samples_macros.xml Sat Nov 28 09:45:44 2020 +0000 @@ -0,0 +1,191 @@ +<macros> + + <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)" /> + <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"/> + </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"/> + <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?" /> + <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 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> + <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="upload_files" type="data" format="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">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="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> + </repeat> + </repeat> + </repeat> + </repeat> + </xml> +</macros>